Anisotropy of electromigration-induced void and island drift.

By means of our novel self-learning kinetic Monte Carlo model (Latz et al 2012 J. Phys.: Condens. Matter 24 485005) we study the electromigration-induced drift of monolayer voids and islands on unpassivated surfaces of single crystalline Ag(111) and Ag(001) films at the atomic scale. Regarding the drift velocity, we find a non-monotonic size dependence for small voids. The drift direction is aligned with the electromigration force only along high symmetry directions, while halfway between, the angle enclosed by them is maximal. The magnitude of these directional deviations strongly depends on the system parameter, which are investigated in detail. The simulation results are in accordance with void motion observed in experiments performed on Ag(111).

From nanoparticles to nanocrystalline bulk: percolation effects in field assisted sintering of silicon nanoparticles.

Nanocrystalline bulk materials are desirable for many applications as they combine mechanical strength and specific electronic transport properties. Our bottom-up approach starts with tailored nanoparticles. Compaction and thermal treatment are crucial, but usually the final stage sintering is accompanied by rapid grain growth which spoils nanocrystallinity. For electrically conducting nanoparticles, field activated sintering techniques overcome this problem. Small grain sizes have been maintained in spite of consolidation. Nevertheless, the underlying principles, which are of high practical importance, have not been fully elucidated yet. In this combined experimental and theoretical work, we show how the developing microstructure during sintering correlates with the percolation paths of the current through the powder using highly doped silicon nanoparticles as a model system. It is possible to achieve a nanocrystalline bulk material and a homogeneous microstructure. For this, not only the generation of current paths due to compaction, but also the disintegration due to Joule heating is required. The observed density fluctuations on the micrometer scale are attributed to the heat profile of the simulated powder networks.

Failure and success of hydrodynamic interaction models.

In suspensions with charged particles, electrostatic forces and hydrodynamic interactions are both important to describe the system. We study different models of hydrodynamic interaction for monopolarly charged particles in a non-polar liquid. In this case, there is no screening of the Coulomb repulsion, so the repulsion between all pairs must be taken into account. The particles are expected to drift away from each other, however at a lower rate when hydrodynamic interaction between the particles is taken into account. Existing, frequently used models of hydrodynamic interactions tend to overestimate the slowing down of the charged particles, even to the extent that the particles effectively attract each other. This is demonstrated for some selected particle setups. We find that these anomalies even occur in dilute systems, if they contain sufficiently many particles. We explain why these anomalies can be avoided by an approach, in which the superposition of interactions is done in the friction tensor instead of the mobility tensor.

Rate equations and scaling in pulsed laser deposition.

We study a simplified model for pulsed laser deposition [Hinnemann, Phys. Rev. Lett. 87, 135701 (2001)] by rate equations. We consider a set of equations where islands are assumed to be pointlike, as well as an improved one that takes the size of the islands into account. The first set of equations is solved exactly but its predictive power is restricted to a few pulses. The improved set of equations is integrated numerically, is in excellent agreement with simulations, and fully accounts for the crossover from continuous to pulsed deposition. Moreover, we analyze the scaling of the nucleation density and show numerical results indicating that a previously observed logarithmic scaling does not apply.

Shear zones in granular materials: optimization in a self-organized random potential.

We introduce a model to describe the wide shear zones observed in modified Couette cell experiments with granular material. The model is a generalization of the recently proposed approach based on a variational principle. The instantaneous shear band is identified with the surface that minimizes the dissipation in a random potential that is biased by the local velocity difference and pressure. The apparent shear zone is the ensemble average of the instantaneous shear bands. The numerical simulation of this model matches excellently with experiments and has measurable predictions.

Morphologies of three-dimensional shear bands in granular media.

We present numerical results on spontaneous symmetry breaking strain localization in axisymmetric triaxial shear tests of granular materials. We simulated shear band formation using the three-dimensional distinct element method with spherical particles. We demonstrate that the local shear intensity, the angular velocity of the grains, the coordination number, and the local void ratio are correlated and any of them can be used to identify shear bands; however, the latter two are less sensitive. The calculated shear band morphologies are in good agreement with those found experimentally. We show that boundary conditions play an important role. We discuss the formation mechanism of shear bands in the light of our observations and compare the results with experiments. At large strains, with enforced symmetry, we found strain hardening.

Effect of variation in herkogamy on outcrossing within a population of Gilia achilleifolia.

The diverse features of floral morphology are often thought to be well-designed mechanisms to manipulate plant mating systems. We evaluated the effectiveness of one such mechanism, anther-stigma separation (herkogamy), in controlling variation in the level of outcrossing among plants in a population of Gilia achilleifolia. Variation in outcrossing rates within populations has the potential to influence the coevolution between inbreeding depression and mating system. Using four polymorphic allozymes, we compared the outcrossing-rate estimates of two groups of individuals under natural conditions: one group with low herkogamy and another with high herkogamy. The high herkogamy group had a higher outcrossing rate (0.572) than the low herkogamy group (0.335). This suggests that the within-population variation in outcrossing rate could potentially cause the previously observed association between herkogamy and inbreeding depression (Takebayashi and Delph, 2000). A previous study of floral traits among G. achilleifolia populations failed to detect a relationship between herkogamy and outcrossing rate, demonstrating that the functionality of traits may be obscured in among-population studies as a consequence of uncontrolled environmental variation. Additionally, the effect of herkogamy on outcrossing rate in delayed selfers such as G. achilleifolia may be particularly prominent when pollinator availability is low. Our population-level estimate of outcrossing rate (0.444) was somewhat lower than an estimate from the same population, 15 years prior to our study (0.75), suggesting that pollinator availability may fluctuate among years. Both within-year and among-year variation in the outcrossing rate may have a strong influence on mating-system evolution.

Piling and avalanches of magnetized particles.

We performed computer simulations based on a two-dimensional distinct element method to study granular systems of magnetized spherical particles. We measured the angle of repose and the surface roughness of particle piles, and we studied the effect of magnetization on avalanching. We report linear dependence of both angle of repose and surface roughness on the ratio f of the magnetic dipole interaction and the gravitational force (interparticle force ratio). There is a difference in avalanche formation at small and at large interparticle force ratios. The transition is at f(c) approximately 7. For f < f(c) small vertical chains follow each other at short times (granular regime), while for f > f(c) the avalanches are typically formed by one single large particle-cluster (correlated regime). The transition is not sharp. We give plausible estimates for f(c) based on stability criteria.

Shear band formation in granular media as a variational problem.

Strain in sheared dense granular material is often localized in a narrow region called the shear band. Recent experiments in a modified Couette cell provided localized shear flow in the bulk away from the confining walls. The nontrivial shape of the shear band was measured as the function of the cell geometry. First, we present a geometric argument for narrow shear bands that connects the function of their surface position with the shape in the bulk. Assuming a simple dissipation mechanism, we show that the principle of minimum dissipation of energy provides a good description of the shape function. Furthermore, we discuss the possibility and behavior of shear bands that are detached from the free surface and are entirely covered in the bulk.

Two-dimensional array of magnetic particles: the role of an interaction cutoff.

Based on theoretical results and simulations, in two-dimensional arrangements of a dense dipolar particle system, there are two relevant local dipole arrangements: (1) a ferromagnetic state with dipoles organized in a triangular lattice and (2) an antiferromagnetic state with dipoles organized in a square lattice. In order to accelerate simulation algorithms, we search for the possibility of cutting off the interaction potential. Simulations on a dipolar two-line system lead to the observation that the ferromagnetic state is much more sensitive to the interaction cutoff R than the corresponding antiferromagnetic state. For R approximately > 8 (measured in particle diameters) there is no substantial change in the energetical balance of the ferromagnetic and antiferromagnetic state and the ferromagnetic state slightly dominates over the antiferromagnetic state, while the situation is changed rapidly for lower interaction cutoff values, leading to the disappearance of the ferromagnetic ground state. We studied the effect of bending ferromagnetic and antiferromagnetic two-line systems and observed that the cutoff has a major impact on the energetical balance of the ferromagnetic and the antiferromagnetic state for R approximately < 4. Based on our results we argue that R approximately 5 is a reasonable choice for dipole-dipole interaction cutoff in two-dimensional dipolar hard sphere systems, if one is interested in local ordering.

Elastic behavior in contact dynamics of rigid particles.

The systematic errors due to the practical implementation of the contact dynamics method for simulation of dense granular media are examined. It is shown that, using the usual iterative solver to simulate a chain of rigid particles, effective elasticity and sound propagation with a finite velocity occur. The characteristics of these phenomena are investigated analytically and numerically in order to assess the limits of applicability of this simulation method and to compare it with soft particle molecular dynamics.

Sex determination in the androdioecious plant Datisca glomerata and its dioecious sister species D. cannabina.

Datisca glomerata is an androdioecious plant species containing male and hermaphroditic individuals. Molecular markers and crossing data suggest that, in both D. glomerata and its dioecious sister species D. cannabina, sex is determined by a single nuclear locus, at which maleness is dominant. Supporting this conclusion, an amplified fragment length polymorphism (AFLP) is heterozygous in males and homozygous recessive in hermaphrodites in three populations of the androdioecious species. Additionally, hermaphrodite x male crosses produced 1:1 sex ratios, while hermaphrodite x hermaphrodite crosses produced almost entirely hermaphroditic offspring. No perfectly sex-linked marker was found in the dioecious species, but all markers associated with sex mapped to a single linkage group and were heterozygous in the male parent. There was no sex-ratio heterogeneity among crosses within D. cannabina collections, but males from one collection produced highly biased sex ratios (94% females), suggesting that there may be sex-linked meiotic drive or a cytoplasmic sex-ratio factor. Interspecific crosses produced only male and female offspring, but no hermaphrodites, suggesting that hermaphroditism is recessive to femaleness. This comparative approach suggests that the hermaphrodite form arose in a dioecious population from a recessive mutation that allowed females to produce pollen.

Unusual scaling for pulsed laser deposition.

We show that a simple model for pulsed laser deposition exhibits an unusual type of scaling behavior for the island density in the submonolayer regime. This quantity is studied as a function of pulse intensity and deposition time. We find a data collapse for the ratios of the logarithms of these quantities, whereas conventional scaling as observed in molecular beam epitaxy involves ratios of powers.

Diabetes: novel therapeutic developments. 21-22 September 1999, London, UK.

The treatment of diabetes represents an extremely active area of new product development. The goal is to effectively regulate glucose in a physiological manner, so as to reduce HbA1c levels and the complications of diabetes. An extremely broad range of new products for the treatment of Type I and/or Type II diabetes are in the pipeline. These include: new forms and methods of delivering insulin to increase compliance; novel pharmaceutical agents to reduce serum glucose and HbA1c levels; immunoregulatory agents which will prevent or reverse diabetic autoimmunity; glucose sensor-insulin pump feedback loops; and, transplantation of xenogeneic islets in immunoprotected microreactors.

Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells.

Fluorescein-labeled oligodeoxynucleotides (oligos) were introduced into cultured rat myoblasts, and their molecular movements inside the nucleus were studied by fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). FCS revealed that a large fraction of both intranuclear oligo(dT) (43%) and oligo(dA) (77%) moves rapidly with a diffusion coefficient of 4 x 10(-7) cm2/s. Interestingly, this rate of intranuclear oligo movement is similar to their diffusion rates measured in aqueous solution. In addition, we detected a large fraction (45%) of the intranuclear oligo(dT), but not oligo(dA), diffusing at slower rates (

Mobility of TrkA is regulated by phosphorylation and interactions with the low-affinity NGF receptor.

The nerve growth factor (NGF) receptor is a complex of two proteins, gp75 and the tyrosine kinase TrkA. Using fluorescence recovery after photobleaching, we have studied the diffusion properties of the TrkA receptor. For PC12 cells that express both gp75 and TrkA, TrkA was relatively immobile with only 28 +/- 1% of receptor molecules free to diffuse with D = (3.64 +/- 0.23) x 10(-9) cm2/s. Addition of NGF decreased the mobile fraction to 21 +/- 1% with D = (4.11 +/- 0.18) x 10(-9) cm2/s. Using the Sf9 baculovirus expression system, we were able to study TrkA in the absence and presence of gp75. On Sf9 cells, TrkA showed a mobile fraction of 46 +/- 2% with D = (2.64 +/- 0.21) x 10(-9) cm2/s in the absence of gp75 and 43 +/- 2% with D = (2.31 +/- 0.25) x 10(-9) cm2/s in its presence. Thus, gp75 did not alter TrkA mobility. Addition of NGF to the medium approximately halved the mobile fraction for TrkA in both the absence and presence of gp75. However, using a kinase-deficient mutant of TrkA, we found that ligand-induced immobilization requires an active kinase in the absence of gp75 but not in its presence. In addition, using point mutations at specific TrkA autophosphorylation sites, we determined that mobility is controlled by multiple phosphorylation sites, but the SHC binding site at Y490 may be particularly important for ligand-induced immobilization of TrkA. Therefore, two mechanisms lead to NGF-induced immobilization of TrkA--the first resulting from autophosphorylation of TrkA and the second occurring through TrkA's association with gp75.

Changes in lipid diffusibility in the hamster sperm head plasma membrane during capacitation in vivo and in vitro.

The technique of fluorescence recovery after photobleaching (FRAP) was employed on spermatozoa labeled with the fluorescent lipid analogue C14dil to provide two measures of lateral diffusion in the plane of the sperm plasma membrane during capacitation in vivo and in vitro: the diffusion coefficient (D) for C14dil and the fraction of C14dil that is free to diffuse (%R) within the domain. To evaluate changes in lipid diffusibility during capacitation in vivo, spermatozoa were recovered from the uterus within 30 min after ejaculation or from the oviduct at 2, 4, 6 and 8 hr after mating. To compare the changes which occur in vivo with those which occur during capacitation in vitro, caudal epididymal spermatozoa were incubated under capacitating or non-capacitating (control) conditions for 4 hr. Although transient changes in D occurred during the course of capacitation, there was no net change in D for either anterior (AH) or posterior head (PH) domains following capacitation in vitro or in vivo. Significant differences in the lipid diffusion coefficient between the two head domains were observed during the course of capacitation. A transient decrease in %R was observed for the AH domain during capacitation in vitro and incubation under control conditions, but no significant change in %R was observed in the AH domain during capacitation in vivo. A significant decline in %R of the PH domain was observed for spermatozoa during capacitation in vivo, in vitro and following incubation under non-capacitating conditions. These data indicate that the changes in the lipid diffusibility of the AH and PH domains which occur during capacitation in vivo exhibit both similarities and differences to those which occur during capacitation in vitro.

Quantitative video microscopy.

Obviously there are many variations and embellishments on the topic of quantitating your image. I have tried here to offer you a very practical guide which highlights some of the critical issues paying particular attention to problems which can prevent or compromise your success. These include: errors due to aspect ratio, use of automatic camera settings, improper setting of dynamic range, and use of integer arithmetic. Further information can be found in several other chapters in this volume as well as in the references below. Additionally you shouldn't overlook the technical manuals which come with your video systems. The field of video microscopy has evolved as a cooperative effort between academia and industry. As a result you will find that many of the technical support personnel from microscope, video, and image processing companies are well versed on the issue of video imaging in biology and are more than willing to assist you.

Fluorescence resonance energy transfer analysis of ribozyme kinetics reveals the mode of action of a facilitator oligonucleotide.

A defining characteristic of catalysts is the rate at which they can process multiple copies of substrate. In the case of synthetic hammerhead ribozymes that cleave an RNA sequence, binding of the ribozyme to the substrate and products is through base-paired duplexes. The kinetics of formation and dissociation of these duplexes can determine the turnover of the ribozyme. We have followed these processes in real time by using fluorescent labels that can interact through fluorescence resonance energy transfer (FRET). This approach has been used to identify the rate-limiting steps for a particular ribozyme and to reveal how turnover was improved by a facilitator oligonucleotide. It was found that dissociation of the ribozyme-substrate complex is faster than cleavage to products. Hence, to undergo cleavage, most substrate molecules must interact with a ribozyme more than once. In the presence of a facilitator oligonucleotide, the complex is stabilized so that cleavage is faster than dissociation. Under these circumstances, cleavage of the substrate becomes the most likely outcome following binding to the ribozyme.

The neurotrophin receptor, gp75, forms a complex with the receptor tyrosine kinase TrkA.

The high-affinity NGF receptor is thought to be a complex of two receptors , gp75 and the tyrosine kinase TrkA, but direct biochemical evidence for such an association had been lacking. In this report, we demonstrate the existence of such a gp75-TrkA complex by a copatching technique. Gp75 on the surface of intact cells is patched with an anti-gp75 antibody and fluorescent secondary antibody, the cells are then fixed to prevent further antibody-induced redistributions, and the distribution of TrkA is probed with and anti-TrkA antibody and fluorescent secondary antibody. We utilize a baculovirus-insect cell expression of wild-type and mutated NGF receptors. TrkA and gp75 copatch in both the absence and presence of NGF. The association is specific, since gp75 does not copatch with other tyrosine kinase receptors, including TrkB, platelet-derived growth factor receptor-beta, and Torso (Tor). To determine which domains of TrkA are required for copatching, we used a series of TrkA-Tor chimeric receptors and show that the extracellular domain of TrkA is sufficient for copatching with gp75. A chimeric receptor with TrkA transmembrane and intracellular domains show partial copatching with gp75. Deletion of the intracellular domain of gp75 decreases but does not eliminate copatching. A point mutation which inactivates the TrkA kinase has no effect on copatching, indicating that this enzymatic activity is not required for association with gp75. Hence, although interactions between the gp75 and TrkA extracellular domains are sufficient for complex formation, interactions involving other receptor domains also play a role.