Efficient generation of diffraction-limited multi-sheet pattern for biological imaging

We demonstrate a new technique to generate multiple light-sheets for fluorescence microscopy. This is possible by illuminating the cylindrical lens using multiple copies of Gaussian beams. A diffraction grating placed just before the cylindrical lens splits the incident Gaussian beam into multiple beams traveling at different angles. Subsequently, this gives rise to diffraction-limited light-sheets after the Gaussian beams pass through the combined cylindrical lens-objective sub-system. Direct measurement of field at and around the focus of objective lens shows multi-sheet pattern with an average thickness of 7.5 mu m and inter-sheet separation of 380 mu m. Employing an independent orthogonal detection sub-system, we successfully imaged fluorescently-coated yeast cells (approximate to 4 mu m) encaged in agarose gel-matrix. Such a diffraction-limited sheet-pattern equipped with dedicated detection system may find immediate applications in the field of optical microscopy and fluorescence imaging. (C) 2015 Optical Society of America

LANDSCAPE DYNAMICS MODELING THROUGH INTEGRATED MARKOV, FUZZY-AHP AND CELLULAR AUTOMATA

Multi temporal land use information were derived using two decades remote sensing data and simulated for 2012 and 2020 with Cellular Automata (CA) considering scenarios, change probabilities (through Markov chain) and Multi Criteria Evaluation (MCE). Agents and constraints were considered for modeling the urbanization process. Agents were nornmlized through fiizzyfication and priority weights were assigned through Analytical Hierarchical Process (AHP) pairwise comparison for each factor (in MCE) to derive behavior-oriented rules of transition for each land use class. Simulation shows a good agreement with the classified data. Fuzzy and AHP helped in analyzing the effects of agents of growth clearly and CA-Markov proved as a powerful tool in modelling and helped in capturing and visualizing the spatiotemporal patterns of urbanization. This provided rapid land evaluation framework with the essential insights of the urban trajectory for effective sustainable city planning.

Crystal Structure and Prediction

The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

Crystal landscape in the orcinol:4,4 `-bipyridine system: synthon modularity, polymorphism and transferability of multipole charge density parameters

Polymorphism in the orcinol: 4,4'-bipyridine cocrystal system is analyzed in terms of a robust convergent modular phenol...pyridine supramolecular synthon. Employing the Synthon Based Fragments Approach (SBFA) to transfer the multipole charge density parameters, it is demonstrated that the crystal landscape can be quantified in terms of intermolecular interaction energies in the five crystal forms so far isolated in this complex system. There are five crystal forms. The first has an open, divergent O-H...N based structure with alternating orcinol and bipyridine molecules. The other four polymorphs have different three-dimensional packing but all of them are similar at an interaction level, and are based on a modular O-H...N mediated supramolecular synthon that consists of two orcinol and two bipyridine molecules in a closed, convergent structure. The SBFA method, which depends on the modularity of synthons, provides good agreement between experiment and theory because it takes into account the supramolecular contribution to charge density. The existence of five crystal forms in this system shows that polymorphism in cocrystals need not be considered to be an unusual phenomenon. Studies of the crystal landscape could lead to an understanding of the kinetic pathways that control the crystallization processes, in other words the valleys in the landscape. These pathways are traditionally not considered in exercises pertaining to computational crystal structure prediction, which rather monitors the thermodynamics of the various stable forms in the system, in other words the peaks in the landscape.

Digital image analysis around isotropic points for photoelastic pattern recognition

Fringe tracking and fringe order assignment have become the central topics of current research in digital photoelasticity. Isotropic points (IPs) appearing in low fringe order zones are often either overlooked or entirely missed in conventional as well as digital photoelasticity. We aim to highlight image processing for characterizing IPs in an isochromatic fringe field. By resorting to a global analytical solution of a circular disk, sensitivity of IPs to small changes in far-field loading on the disk is highlighted. A local theory supplements the global closed-form solutions of three-, four-, and six-point loading configurations of circular disk. The local theoretical concepts developed in this paper are demonstrated through digital image analysis of isochromatics in circular disks subjected to three-and four-point loads. (C) 2015 Society of Photo-Optical Instrumentation Engineers (SPIE)

Pattern-Formation During Self-organization in Three-Phase Eutectic Solidification

Eutectic growth is an interesting example for exploring the topic of pattern-formation in multi-phase systems, where the growth of the phases is coupled with the diffusive transport of one or more components in the melt. While in the case of binary alloys, the number of possibilities are limited (lamellae, rods, labyrinth etc.), their number rapidly increases with the number of components and phases. In this paper, we will investigate pattern formation during three-phase eutectic solidification using a state-of-the art phase-field method based on the grand-canonical density formulation. The major aim of the study is to highlight the role of two properties, which are the volume fraction of the solid phases and the solid-liquid interfacial energies, in the self-organization of the solid phases during directional growth. Thereafter, we will show representative phase-field simulations of a micro-structure in a real alloy (Ag-Al-Cu) using an asymmetric phase diagram as well as interfacial properties.

Relationship between entropy and diffusion: A statistical mechanical derivation of Rosenfeld expression for a rugged energy landscape

Diffusion-a measure of dynamics, and entropy-a measure of disorder in the system are found to be intimately correlated in many systems, and the correlation is often strongly non-linear. We explore the origin of this complex dependence by studying diffusion of a point Brownian particle on a model potential energy surface characterized by ruggedness. If we assume that the ruggedness has a Gaussian distribution, then for this model, one can obtain the excess entropy exactly for any dimension. By using the expression for the mean first passage time, we present a statistical mechanical derivation of the well-known and well-tested scaling relation proposed by Rosenfeld between diffusion and excess entropy. In anticipation that Rosenfeld diffusion-entropy scaling (RDES) relation may continue to be valid in higher dimensions (where the mean first passage time approach is not available), we carry out an effective medium approximation (EMA) based analysis of the effective transition rate and hence of the effective diffusion coefficient. We show that the EMA expression can be used to derive the RDES scaling relation for any dimension higher than unity. However, RDES is shown to break down in the presence of spatial correlation among the energy landscape values. (C) 2015 AIP Publishing LLC.

Pattern formation in thin films of polymer solutions: Theory and simulations

Self-assembly has been recognized as an efficient tool for generating a wide range of functional, chemically, or physically textured surfaces for applications in small scale devices. In this work, we investigate the stability of thin films of polymer solutions. For low concentrations of polymer in the solution, long length scale dewetting patterns are obtained with wavelength approximately few microns. Whereas, for concentrations above a critical value, bimodal dispersion curves are obtained with the dominant wavelength being up to two orders smaller than the usual dewetting length scale. We further show that the short wavelength corresponds to the phase separation in the film resulting in uniformly distributed high and low concentration regions. Interestingly, due to the solvent entropy, at very high concentration values of polymer, a re-entrant behaviour is observed with the dominant length scale now again corresponding to the dewetting wavelength. Thus, we show that the binary films of polymer solutions provide additional control parameters that can be utilized for generating functional textured surfaces for various applications. (C) 2016 AIP Publishing LLC.

Increasing Critical Sensitivity of the Load/Unload Response Ratio before Large Earthquakes with Identified Stress Acclumulation Pattern

The Load/Unload Response Ratio (LURR) method is proposed for short-to-intermediate-term earthquake prediction [Yin, X.C., Chen, X.Z., Song, Z.P., Yin, C., 1995. A New Approach to Earthquake Prediction — The Load/Unload Response Ratio (LURR) Theory, Pure Appl. Geophys., 145, 701–715]. This method is based on measuring the ratio between Benioff strains released during the time periods of loading and unloading, corresponding to the Coulomb Failure Stress change induced by Earth tides on optimally oriented faults. According to the method, the LURR time series usually climb to an anomalously high peak prior to occurrence of a large earthquake. Previous studies have indicated that the size of critical seismogenic region selected for LURR measurements has great influence on the evaluation of LURR. In this study, we replace the circular region usually adopted in LURR practice with an area within which the tectonic stress change would mostly affect the Coulomb stress on a potential seismogenic fault of a future event. The Coulomb stress change before a hypothetical earthquake is calculated based on a simple back-slip dislocation model of the event. This new algorithm, by combining the LURR method with our choice of identified area with increased Coulomb stress, is devised to improve the sensitivity of LURR to measure criticality of stress accumulation before a large earthquake. Retrospective tests of this algorithm on four large earthquakes occurred in California over the last two decades show remarkable enhancement of the LURR precursory anomalies. For some strong events of lesser magnitudes occurred in the same neighborhoods and during the same time periods, significant anomalies are found if circular areas are used, and are not found if increased Coulomb stress areas are used for LURR data selection. The unique feature of this algorithm may provide stronger constraints on forecasts of the size and location of future large events.

Experimental Study of Surface Deformation and Flow Pattern on Buoyant-Thermocapillary Convection

Free surface deformation is one of the most important physical phenomena in fluids with free surface. In the present paper, convection and surface deformation caused by thermocapillary effect in a rectangular cavity were investigated. In ground experiments, the convection was also affected by gravity. The cavity has a horizontal cross section of 52mm×42mm and the thikkness of the liquid layer is 4mm. Temperature difference between two sides of the liquid layer was increased gradually, and the flow in liquid layer will develop from steady to unstable convection. An optical diagnostic system consisting of a revised Michelson interferometer with image processor was developed to study fluid surface deformation in convection, and the displacements of free surface oscillation were determined. PIV technique was adopted to observe the evolution of flow pattern, and the velocity fields were obtained quantitatively. The present experiments demonstrate that surface deformation is quite distinct in buoyant-thermocapillary convection. in order to understand the mechanism of buoyant-thermocapillary convection, not only the hydrothermal wave instability but also the surface wave instability should be discussed.

New tools for self-organised pattern formation

Position-dependent gene expression is a critical aspect of the development and behaviour of multicellular organisms. It requires a complex series of interactions to occur between different cell types in addition to intracellular signalling cascades. We used Escherichia coli to study the properties of an artificial signalling system at the interface between two expanding cell populations. We genetically engineered one population to produce a diffusible acyl-homoserine lactone (AHL) signal, and another population to respond to it. Our experiments demonstrate how such a signal can be used to reproducibly generate simple visible patterns with high accuracy in swimming agar. The producing and responding cassettes of two such signalling systems can be linked to produce a symmetric interface for bidirectional communication that can be used to visualise molecular logic. Intracellular feedback between these two cassettes would then create a framework for self-organised patterning of higher complexity. Adapting the experiments of Basu et al. (Basu et al., 2005) using cell motility, rather than a differential response to AHL concentrations as a way to define zones of response, we noted how the interaction of sender and receiver cell populations on a swimming plate could lead to complex pattern formation. Equipping highly motile strains such as E. coli MC1000 with AHL-mediated auto-inducing systems based on Vibrio fischeri luxI/luxR and Pseudomonas aeruginosa lasI/lasR cassettes would allow the amplification of a response to an AHL signal and its propagation. We designed and synthesised codon-optimised auto-inducing luxI/R and lasI/R cassettes as optimal gene expression is crucial for the generation of robust patterns. We still have to complete and test the entire genetic circuitry, although by modelling the system we were able to demonstrate its feasibility. © 2007 The Institution of Engineering and Technology.

Pattern formation and spatial solitons in bistable liquid-crystal microcavities

We report on spatial pattern formation, and appearances of 'optical bullet holes' in single-mode microcavities that are filled with liquid-crystals, when pumped above the cavity resonance frequency. These phenomena only occur beyond the bistability threshold. ©2002 Optical Society of America.

Pattern Recognition With Weighted Complex Networks

In this paper we introduce a weighted complex networks model to investigate and recognize structures of patterns. The regular treating in pattern recognition models is to describe each pattern as a high-dimensional vector which however is insufficient to express the structural information. Thus, a number of methods are developed to extract the structural information, such as different feature extraction algorithms used in pre-processing steps, or the local receptive fields in convolutional networks. In our model, each pattern is attributed to a weighted complex network, whose topology represents the structure of that pattern. Based upon the training samples, we get several prototypal complex networks which could stand for the general structural characteristics of patterns in different categories. We use these prototypal networks to recognize the unknown patterns. It is an attempt to use complex networks in pattern recognition, and our result shows the potential for real-world pattern recognition. A spatial parameter is introduced to get the optimal recognition accuracy, and it remains constant insensitive to the amount of training samples. We have discussed the interesting properties of the prototypal networks. An approximate linear relation is found between the strength and color of vertexes, in which we could compare the structural difference between each category. We have visualized these prototypal networks to show that their topology indeed represents the common characteristics of patterns. We have also shown that the asymmetric strength distribution in these prototypal networks brings high robustness for recognition. Our study may cast a light on understanding the mechanism of the biologic neuronal systems in object recognition as well.

Fractal Pattern Formation In Anodic Bonding Of Pyrex Glass/Al/Si

Anodic bonding of Pyrex glass/Al/Si is an important bonding technique in micro/nanoelectromechanical systems (MEMS/NEMS) industry. The anodic bonding of Pyrex 7740 glass/Aluminum film/Silicon is completed at the temperature from 300 degrees C to 375 degrees C with a bonding voltage between 150 V and 450 V. The fractal patterns are formed in the intermediate Al thin film. This pattern has the fractal dimension of the typical two-dimensional diffusion-limited aggregation (2D DLA) process, and the fractal dimension is around 1.7. The fractal patterns consist of Al and Si crystalline grains, and their occurrences are due to the limited diffusion, aggregation, and crystallization of Si and Al atoms in the intermediate Al layers. The formation of the fractal pattern is helpful to enhance the bonding strength between the Pyrex 7740 glass and the aluminum thin film coated on the crystal silicon substrates.