Quantum to classical crossover in the 2D easy-plane XXZ model

Ground-state and thermodynamical properties of the spin-1/2 two-dimensional easy-plane XXZ model are investigated by both a Green's-function approach and by Lanczos diagonalizations on lattices with up to 36 sites. We calculate the spatial and temperature dependences of various spin correlation functions, as well as the wave-vector dependence of the spin susceptibility for all anisotropy parameters $\Delta$. In the easy--plane ferromagnetic region $(-1< \Delta < 0)$, the longitudinal correlators of spins at distance $r$ change sign at a finite temperature $T_0(\Delta, {\bf r})$. This transition, observed in the 2D case for the first time, can be interpreted as a quantum to classical crossover.Comment: 4 pages, 6 figures, Contribution to the Ising Centennial Colloquium, ICM2000, Belo Horizonte, Brazil, August 200

Theory of short-range magnetic order for the t-J model

We present a self-consistent theory of magnetic short-range order based on a spin-rotation-invariant slave-boson representation of the 2D t-J model. In the functional-integral scheme, at the nearest-neighbour pair-approximation level, the bosonized t-J Lagrangian is transformed to a classical Heisenberg model with an effective (doping-dependent) exchange interaction which takes into account the interrelation of ``itinerant'' and ``localized'' magnetic behaviour. Evaluating the theory in the saddle-point approximation, we find a suppression of antiferromagnetic and incommensurate spiral long-range-ordered phases in the favour of a paramagnetic phase with pronounced antiferromagnetic short-range correlations.Comment: 2 pages, 1 Postscript figure, LTpaper.sty, Proc. XXI Int. Conf. on Low Temp. Phys. Prague 9

Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states

Magnetic order in the quasi-two-dimensional easy-plane XXZ model

A Green's-function theory of antiferromagnetic short-range and long-range order (LRO) in the $S=1/2$ quasi-two-dimensional easy-plane XXZ model is presented. As the main new result, {\it two} phase transitions due to the combined influence of spatial and spin anisotropy are found, where below the higher and lower N\'{e}el temperature there occurs LRO in the transverse and in both the transverse and longitudinal spin correlators, respectively. Comparing the theory with neutron-scattering data for the correlation length of $\rm La_2CuO_4$, a very good agreement in the whole temperature dependence is obtained. Moreover, for $\rm La_2CuO_4$, $\rm Sr_2CuO_2Cl_2$, and $\rm Ca_{0.85}Sr_{0.15}CuO_2$ the second phase with longitudinal LRO is predicted to appear far below room temperature.Comment: 7 pages, 5 figure

A high-level 3D visualization API for Java and ImageJ

BACKGROUND: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. RESULTS: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. CONCLUSIONS: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de

Efficient Bayesian-based Multi-View Deconvolution

Light sheet fluorescence microscopy is able to image large specimen with high resolution by imaging the sam- ples from multiple angles. Multi-view deconvolution can significantly improve the resolution and contrast of the images, but its application has been limited due to the large size of the datasets. Here we present a Bayesian- based derivation of multi-view deconvolution that drastically improves the convergence time and provide a fast implementation utilizing graphics hardware.Comment: 48 pages, 20 figures, 1 table, under review at Nature Method

High-resolution computed tomography reconstructions of invertebrate burrow systems

The architecture of biogenic structures can be highly influential in determining species contributions to major soil and sediment processes, but detailed 3-D characterisations are rare and descriptors of form and complexity are lacking. Here we provide replicate high-resolution micro-focus computed tomography (μ-CT) data for the complete burrow systems of three co-occurring, but functionally contrasting, sediment-dwelling inter-tidal invertebrates assembled alone, and in combination, in representative model aquaria. These data (≤2,000 raw image slices aquarium−1, isotropic voxel resolution, 81 μm) provide reference models that can be used for the development of novel structural analysis routines that will be of value within the fields of ecology, pedology, geomorphology, palaeobiology, ichnology and mechanical engineering. We also envisage opportunity for those investigating transport networks, vascular systems, plant rooting systems, neuron connectivity patterns, or those developing image analysis or statistics related to pattern or shape recognition. The dataset will allow investigators to develop or test novel methodology and ideas without the need to generate a complete three-dimensional computation of exemplar architecture

New insights into the nature of semi-soft elasticity and “mechanical-Fréedericksz transitions” in liquid crystal elastomers

The mechanical properties of an all-acrylate Liquid Crystal Elastomer (LCE) with a glass transition of 14±1°C are reported. The highly nonlinear load curve has a characteristic shape associated with semi-soft elasticity (SSE). Conversely, measurements of the director orientation throughout tensile loading instead indicate a “mechanical-Fréedericksz” transition (MFT). Values of the step length anisotropy, r, are independently calculated from the theories of SSE (r= 3.2±0.4), MFT (9.3<r<30.0) and thermally-induced length change (r=3.8±0.5). From simultaneously recorded polarising microscopy textures, the consequences of the above discrepancies are considered. Further, a mechanically-induced negative order parameter is observed. Results show the tensile load curve shape cannot solely be used to determine the underlying physics. Consequently, the LCE properties cannot be fully described by theories of SSE or MFTs alone. This suggests that the theory of LCEs is not yet complete. The conclusions suggest that both the LC order parameter and r must be functions of the mechanical deformation

High-throughput spheroid screens using volume, resazurin reduction and acid phosphatase activity

Mainstream adoption of physiologically-relevant three-dimensional models has been slow in the last 50 years due to long, manual protocols with poor reproducibility, high price and closed commercial platforms. This chapter describes high-throughput, low-cost, open methods for spheroid viability assessment which use readily-available reagents and open-source software to analyse spheroid volume, metabolism and enzymatic activity. We provide two ImageJ macros for automated spheroid size determination - for both single images and for images in stacks. We also share an Excel template spreadsheet allowing users to rapidly process spheroid size data, analyse plate uniformity (such as edge effects and systematic seeding errors), detect outliers and calculate dose-response. The methods would be useful to researchers in preclinical and translational research planning to move away from simplistic monolayer studies and explore 3D spheroid screens for drug safety and efficacy without substantial investment in money or time