Self-organized defect strings in two-dimensional crystals

Using experiments with single particle resolution and computer simulations we study the collective behaviour of multiple vacancies injected into two-dimensional crystals. We find that the defects assemble into linear strings that propagate through the crystal in a succession of rapid one-dimensional gliding phases and rare rotations, during which the direction of motion changes. At both ends, strings are terminated by dislocations with anti-parallel Burgers vectors. By monitoring the separation of the dislocations, we measure their effective interactions with high precision, for the first time beyond spontaneous formation and annihilation, and explain the double-well form of the dislocation interaction in terms of continuum elasticity theory. Our results give a detailed picture of the motion and interaction of dislocations in two dimensions and enhance our understanding of topological defects in two-dimensional nano-materials

Entropy and Kinetics of Point-Defects in Two-Dimensional Dipolar Crystals

We study in experiment and with computer simulation the free energy and the kinetics of vacancy and interstitial defects in two-dimensional dipolar crystals. The defects appear in different local topologies which we characterize by their point group symmetry; $C_n$ is the n-fold cyclic group and $D_n$ is the dihedral group, including reflections. The frequency of different local topologies is not determined by their almost degenerate energies but dominated by entropy for symmetric configurations. The kinetics of the defects is fully reproduced by a master equation in a multi-state Markov model. In this model, the system is described by the state of the defect and the time evolution is given by transitions occurring with particular rates. These transition rate constants are extracted from experiments and simulations using an optimisation procedure. The good agreement between experiment, simulation and master equation thus provides evidence for the accuracy of the model.Comment: 9 pages, 12 figure

Dissecting the impact of Frizzled receptors in Wnt/beta-catenin signaling of human mesenchymal stem cells

Wnt/beta-catenin signaling is of fundamental importance in the regulation of self-renewal, migration/invasion, and differentiation of human mesenchymal stem cells (hMSCs). Because little information is available about the function of Frizzled receptors (Fzds) as the main receptors of Wnt proteins in hMSCs, we first performed comparative Fzd mRNA expression profiling. Fzd9 and Fzd10 were not expressed in hMSCs. While Fzd3 was expressed at low levels in hMSCs, the other Fzds exhibited high expression rates. Activation and repression of Wnt signaling in hMSCs revealed that the expression levels of Fzd1, Fzd6, and Fzd7 are positively correlated with the Wnt/beta-catenin activation status, whereas Fzd8 exhibited an inverse relation. For studying the functional relevance of Fzds in Wnt/beta-catenin signaling, RNA interference, ectopic expression studies, and rescue approaches were performed in hMSCs carrying a highly sensitive TCF/LEF reporter gene system (Gaussia luciferase). We found that, Fzd1, Fzd5, Fzd7, and Fzd8 are largely involved in Wnt/beta-catenin signaling of hMSCs. Moreover, the knockdown of Fzd5 can be compensated by the ectopic expression of Fzd7. Conversely, the ectopic expression of Fzd5 in Fzd7-knockdown hMSCs resulted in a rescue of Wnt/beta-catenin signaling, pointing to a functional redundancy of Fzd5 and Fzd7

Negotiating the Maze: Case based, Collaborative Distance Learning in Dentistry

The module was developed as an elective to give motivated senior dental students an opportunity to expand their horizons in planning oral rehabilitation. It comprised one tutor and 12 students, from five universities world-wide, communicating on the World Wide Web (WWW), to develop oral rehabilitation plans for simulated patients. Trigger material came from one of two Case Profiles and consisted of diagnostic casts and details of the clinical and radiographic examination in WWW/CD-ROM form. No background material was supplied as to the "patient's" age, sex, history or main concern(s). Students worked in groups of three, each student from a different location. Individual students were given a role within the group: "Patient", who developed a "personal background" belonging to the trigger examination material, "Academic" who identified state-of-the-art treatment options available for the dental treatment needs identified by the group and "General Practitioner" who tailored these options to the "patient's" needs and wants. Student feedback focused on their perception of their experience with the program in response to a questionnaire comprising 11 structured and four "open" questions. All students felt that the program increased their confidence in planning oral rehabilitation. Ten students felt that the "best thing about the program" was the interaction with students from other universities and the exposure to different philosophies from the different schools. Eight students mentioned their increased awareness of the importance of patient input into holistic planning. Under the heading "What was the worst thing", students cited some technical hitches and the snowball effect of two sluggish students who were not identified early enough and thus impacted negatively on the working of their groups. Student feedback showed that the module succeeded in its aims but needed modification to improve the logistics of working with an extended campu

Phylogenetics from paralogs

Motivation: Sequence-based phylogenetic approaches heavily rely on initial data sets to be composed of orthologous sequences only. Paralogs are treated as a dangerous nuisance that has to be detected and removed. Recent advances in mathematical phylogenetics, however, have indicated that gene duplications can also convey meaningful phylogenetic information provided orthologs and paralogs can be distinguished with a degree of certainty. Results: We demonstrate that plausible phylogenetic trees can be inferred from paralogy information only. To this end, tree-free estimates of orthology, the complement of paralogy, are first corrected to conform cographs and then translated into equivalent event-labeled gene phylogenies. A certain subset of the triples displayed by these trees translates into constraints on the species trees. While the resolution is very poor for individual gene families, we observe that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees of several groups of eubacteria. The novel method introduced here relies on solving three intertwined NP-hard optimization problems: the cograph editing problem, the maximum consistent triple set problem, and the least resolved tree problem. Implemented as Integer Linear Program, paralogy-based phylogenies can be computed exactly for up to some twenty species and their complete protein complements. Availability:The ILP formulation is implemented in the Software ParaPhylo using IBM ILOG CPLEX (TM) Optimizer 12.6 and is freely available from http://pacosy.informatik.uni-leipzig.de/paraphyl

Microcanonical quantum fluctuation theorems

Previously derived expressions for the characteristic function of work performed on a quantum system by a classical external force are generalized to arbitrary initial states of the considered system and to Hamiltonians with degenerate spectra. In the particular case of microcanonical initial states explicit expressions for the characteristic function and the corresponding probability density of work are formulated. Their classical limit as well as their relations to the respective canonical expressions are discussed. A fluctuation theorem is derived that expresses the ratio of probabilities of work for a process and its time reversal to the ratio of densities of states of the microcanonical equilibrium systems with corresponding initial and final Hamiltonians.From this Crooks-type fluctuation theorem a relation between entropies of different systems can be derived which does not involve the time reversed process. This entropy-from-work theorem provides an experimentally accessible way to measure entropies.Comment: revised and extended versio