Free energies, vacancy concentrations and density distribution anisotropies in hard--sphere crystals: A combined density functional and simulation study

We perform a comparative study of the free energies and the density distributions in hard sphere crystals using Monte Carlo simulations and density functional theory (employing Fundamental Measure functionals). Using a recently introduced technique (Schilling and Schmid, J. Chem. Phys 131, 231102 (2009)) we obtain crystal free energies to a high precision. The free energies from Fundamental Measure theory are in good agreement with the simulation results and demonstrate the applicability of these functionals to the treatment of other problems involving crystallization. The agreement between FMT and simulations on the level of the free energies is also reflected in the density distributions around single lattice sites. Overall, the peak widths and anisotropy signs for different lattice directions agree, however, it is found that Fundamental Measure theory gives slightly narrower peaks with more anisotropy than seen in the simulations. Among the three types of Fundamental Measure functionals studied, only the White Bear II functional (Hansen-Goos and Roth, J. Phys.: Condens. Matter 18, 8413 (2006)) exhibits sensible results for the equilibrium vacancy concentration and a physical behavior of the chemical potential in crystals constrained by a fixed vacancy concentration.Comment: 17 pages, submitted to Phys. Rev.

Fragility and compressibility at the glass transition

Isothermal compressibilities and Brillouin sound velocities from the literature allow to separate the compressibility at the glass transition into a high-frequency vibrational and a low-frequency relaxational part. Their ratio shows the linear fragility relation discovered by x-ray Brillouin scattering [1], though the data bend away from the line at higher fragilities. Using the concept of constrained degrees of freedom, one can show that the vibrational part follows the fragility-independent Lindemann criterion; the fragility dependence seems to stem from the relaxational part. The physical meaning of this finding is discussed. [1] T. Scopigno, G. Ruocco, F. Sette and G. Monaco, Science 302, 849 (2003)Comment: 4 pages, 2 figures, 2 tables, 33 references. Slightly changed after refereein

Potts-Percolation-Gauss Model of a Solid

We study a statistical mechanics model of a solid. Neighboring atoms are connected by Hookian springs. If the energy is larger than a threshold the "spring" is more likely to fail, while if the energy is lower than the threshold the spring is more likely to be alive. The phase diagram and thermodynamic quantities, such as free energy, numbers of bonds and clusters, and their fluctuations, are determined using renormalization-group and Monte-Carlo techniques.Comment: 10 pages, 12 figure

Many-body interactions and melting of colloidal crystals

We study the melting behavior of charged colloidal crystals, using a simulation technique that combines a continuous mean-field Poisson-Boltzmann description for the microscopic electrolyte ions with a Brownian-dynamics simulation for the mesoscopic colloids. This technique ensures that many-body interactions between the colloids are fully taken into account, and thus allows us to investigate how many-body interactions affect the solid-liquid phase behavior of charged colloids. Using the Lindemann criterion, we determine the melting line in a phase-diagram spanned by the colloidal charge and the salt concentration. We compare our results to predictions based on the established description of colloidal suspensions in terms of pairwise additive Yukawa potentials, and find good agreement at high-salt, but not at low-salt concentration. Analyzing the effective pair-interaction between two colloids in a crystalline environment, we demonstrate that the difference in the melting behavior observed at low salt is due to many-body interactions

Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region

The design and use of a pilot microarray for transcriptome analysis of the symbiotic, nitrogen-fixing Bradyrhizobium japonicum is reported here. The custom-synthesized chip (Affymetrix GeneChip®) features 738 genes, more than half of which belong to a 400-kb chromosomal segment strongly associated with symbiosis-related functions. RNA was isolated following an optimized protocol from wild-type cells grown aerobically and microaerobically, and from cells of aerobically grown regR mutant and microaerobically grown nifA mutant. Comparative microarray analyses thus revealed genes that are transcribed in either a RegR- or a NifA-dependent manner plus genes whose expression depends on the cellular oxygen status. Several genes were newly identified as members of the RegR and NifA regulons, beyond genes, which had been known from previous work. A comprehensive transcription analysis was performed with one of the new RegR-controlled genes (id880). Expression levels determined by microarray analysis of selected NifA- and RegR-controlled genes corresponded well with quantitative real-time PCR data, demonstrating the high complementarity of microarray analysis to classical methods of gene expression analysis in B. japonicum. Nevertheless, several previously established members of the NifA regulon were not detected as transcribed genes by microarray analysis, confirming the potential pitfalls of this approach also observed by other authors. By and large, this pilot study has paved the way towards the genome-wide transcriptome analysis of the 9.1-Mb B. japonicum genom

Effect of a thin AlO_x layer on transition-edge sensor properties

We have studied the physics of transition-edge sensor (TES) devices with an insulating AlOx layer on top of the device to allow implementation of more complex detector geometries. By comparing devices with and without the insulating film, we have observed significant additional noise apparently caused by the insulator layer. In addition, AlOx was found to be a relatively good thermal conductor. This adds an unforeseen internal thermal feature to the system.Comment: 6 pages, 5 figures, Low Temperature Detectors 14 conferenc

Grain Size seperation and sediment mixing in Artic Ocean sediments: evidence from the strontium isotope systematic

The (87)Rb/(86)Sr and (87)Sr/(86)Sr ratios of Laptev Sea sediments, of Arctic Ocean sediments and of suspended particulate matter (SPM) from Siberian rivers (Lena and Khatanga) form 'pseudo-isochrons' due to grain-size separation processes which are referred to as 'Lena Mixing Envelope' (LME) and as 'Flood Basalt Envelope' (FBE). At the land-ocean transition the reduction of the particle velocity causes a deposition of coarser grained material and the contact with saline water enhances a precipitation of finer-grained material. The coarse-grained material is enriched in Sr showing less radiogenic (87)Sr/(86)Sr ratios whereas fine grained material is depleted in Sr relative to Rb showing more radiogenic (87)Sr/(86)Sr ratios, The experimentally determined spread of the (87)Rb/(86)Sr and (87)Sr/(86)Sr ratios as a function of grain size in one sediment sample is on the same order as the natural spread of the (87)Sr/(86)Sr ratios observed in all samples from the Arctic Ocean. Chemical Index of Alteration (CIA) for the Lena river SPM tend to confirm previous observations that chemical alteration is negligible in the Arctic environment. Thus, these 'pseudo-isochrons' reflect an average age and the average isotope composition in the river drainage area. Calculated apparent ages from the FBE reflect the age of the Siberian flood basalt of about 220 Ma and the initial ratio of 0.707(1) reflects their mantle origin. The age calculated from the LME of about 125 Ma reflects accidentally the Jurassic and Cretaceous age of the sediments drained by the Lena river and the initial ratio of 0.714(1) reflects the crustal origin of their source rocks. Comparison of geographical locations reveals that all samples from the eastern Laptev Sea (east of 120 degrees E) fall along the LME whereas all samples from the western Laptev Sea (west of 120 degrees E) fall between LME and FBE. Mixing calculations based on (143)Nd/(144)Nd measurements, not influenced by grain size, show that about 75% of the western Laptev Sea sediments originate from the Lena drainage area whereas about 25% of the sediments are delivered from the Siberian flood basalt province. Sediments from the central Arctic Ocean are isotopically related to the Lena drainage area and the Siberian flood basalt province. However, sediments from the Arctic Ocean margins close to Novaya Semlya, Greenland, the Fram Strait and Svalbard originate from sources not yet identified. (C) 1999 Elsevier Science B.V. All rights reserved

Instability of insulating states in optical lattices due to collective phonon excitations

The role of collective phonon excitations on the properties of cold atoms in optical lattices is investigated. These phonon excitations are collective excitations, whose appearance is caused by intersite atomic interactions correlating the atoms, and they do not arise without such interactions. These collective excitations should not be confused with lattice vibrations produced by an external force. No such a force is assumed. But the considered phonons are purely self-organized collective excitations, characterizing atomic oscillations around lattice sites, due to intersite atomic interactions. It is shown that these excitations can essentially influence the possibility of atoms to be localized. The states that would be insulating in the absence of phonon excitations can become delocalized when these excitations are taken into account. This concerns long-range as well as local atomic interactions. To characterize the region of stability, the Lindemann criterion is used.Comment: Latex file, 27 pages, 1 figur

Self-organized Beating and Swimming of Internally Driven Filaments

We study a simple two-dimensional model for motion of an elastic filament subject to internally generated stresses and show that wave-like propagating shapes which can propel the filament can be induced by a self-organized mechanism via a dynamic instability. The resulting patterns of motion do not depend on the microscopic mechanism of the instability but only of the filament rigidity and hydrodynamic friction. Our results suggest that simplified systems, consisting only of molecular motors and filaments could be able to show beating motion and self-propulsion.Comment: 8 pages, 2 figures, REVTe

Immersed nano-sized Al dispersoids in an Al matrix; effects on the structural and mechanical properties by Molecular Dynamics simulations

We used molecular dynamics simulations based on a potential model in analogy to the Tight Binding scheme in the Second Moment Approximation to simulate the effects of aluminum icosahedral grains (dispersoids) on the structure and the mechanical properties of an aluminum matrix. First we validated our model by calculating several thermodynamic properties referring to the bulk Al case and we found good agreement with available experimental and theoretical data. Afterwards, we simulated Al systems containing Al clusters of various sizes. We found that the structure of the Al matrix is affected by the presence of the dispersoids resulting in well ordered domains of different symmetries that were identified using suitable Voronoi analysis. In addition, we found that the increase of the grain size has negative effect on the mechanical properties of the nanocomposite as manifested by the lowering of the calculated bulk moduli. The obtained results are in line with available experimental data.Comment: 15 pages, 8 figures. Submitted to J. Phys: Condens. Matte