ALWIN-Algorithmic Wiswesser Notation System for Organic Compounds

ALWIN, a new chemical notation system for organic compounds, based on the Wiswesser Line Notation, is described. Procedures and rules are given for constructing ALWIN for acyclic structures and cyclic structures, vi.?., benzene and Its derivatives, monocyclic, bicyclic, polycyclic, perifused, splro, bridged ring, and ring of rlngs systems. A new method called "tessellation" is introduced for the topological descrlptlon of fused and spiro ring systems. Also new concepts are introduced for describing bridged ring and ring of rlngs systems.

New measures for estimating surface complementarity and packing at protein-protein interfaces

A number of methods exist that use different approaches to assess geometric properties like the surface complementarity and atom packing at the protein-protein interface. We have developed two new and conceptually different measures using the Delaunay tessellation and interface slice selection to compute the surface complementarity and atom packing at the protein-protein interface in a straightforward manner. Our measures show a strong correlation among themselves and with other existing measures, and can be calculated in a highly time-efficient manner. The measures are discriminative for evaluating biological, as well as non-biological protein-protein contacts, especially from large protein complexes and large-scale structural studies(http://pallab.serc. iisc.ernet.in/nip_nsc). (C) 201 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

Relation Between the Diffusivity, Viscosity, and Ionic Radius of LiCl in Water, Methanol, and Ethylene Glycol: A Molecular Dynamics Simulation

A molecular dynamics (MD) investigation of LiCl in water, methanol, and ethylene glycol (EG) at 298 K is reported. Several; structural and dynamical properties of the ions as well as the solvent such as self-diffusivity, radial distribution functions, void and neck distributions, velocity autocorrelation functions, and mean residence times of solvent in the first solvation shell have been computed. The results show that the reciprocal relationship between the self-diffusivity of the ions and the viscosity is valid in almost all solvents with the exception of water. From an analysis of radial distribution functions and coordination numbers the nature of hydrogen bonding within the solvent and its influence on the void and neck distribution becomes evident. It is seen that the solvent solvent interaction is important in EG while solute solvent interactions dominate in water and methanol. From Voronoi tessellation, it is seen that the voids and necks within methanol are larger as compared to those within water or EG. On the basis of the void and neck distributions obtained from MD simulations and literature experimental data of limiting ion conductivity for various ions of different sizes we show that there is a relation between the void and neck radius on e one hand and dependence of conductivity on the ionic radius on the other. It is shown that the presence of large diameter voids and necks in methanol is responsible for maximum in limiting ion conductivity (lambda(0)) of TMA(+), while in water in EG, the maximum is seen for Rb+. In the case of monovalent anions, maximum in lambda(0) as a function ionic radius is seen for Br- in water EG but for the larger ClO4- ion in methanol. The relation between the void and neck distribution and the variation in lambda(0) with ionic radius arises via the Levitation effect which is discussed. These studies show the importance of the solvent structure and the associated void structure.

Étude des transitions de phases dans le modèle de Higgs abélien en (2+1) dimensions et l'effet du terme de Chern-Simons

Nous avons investigué, via les simulations de Monte Carlo, les propriétés non-perturbatives du modèle de Higgs abélien en 2+1 dimensions sans et avec le terme de Chern-Simons dans la phase de symétrie brisée, en termes de ses excitations topologiques: vortex et anti-vortex. Le but du présent travail est de rechercher les phases possibles du système dans ce secteur et d'étudier l'effet du terme de Chern-Simons sur le potentiel de confinement induit par les charges externes trouvé par Samuel. Nous avons formulé une description sur réseau du modèle effectif en utilisant une tesselation tétraédrique de l'espace tridimensionnel Euclidien pour générer des boucles de vortex fermées. En présence du terme de Chern-Simons, dans une configuration donnée, nous avons formulé et calculé le nombre d'enlacement entre les différentes boucles de vortex fermées. Nous avons analysé les propriétés du vide et calculé les valeurs moyennes de la boucle de Wilson, de la boucle de Polyakov à différentes températures et de la boucle de 't Hooft en présence du terme de Chern-Simons. En absence du terme de Chern-Simons, en variant la masse des boucles de vortex, nous avons trouvé deux phases distinctes dans le secteur de la symétrie brisée, la phase de Higgs habituelle et une autre phase caractérisée par l'apparition de boucles infinies. D'autre part, nous avons trouvé que la force entre les charges externes est écrantée correpondant à la loi périmètre pour la boucle de Wilson impliquant qu'il n'y a pas de confinement. Cependant, après la transition, nous avons trouvé qu'il existe toujours une portion de charges externes écrantée, mais qu'après une charge critique, l'énergie libre diverge. En présence du terme de Chern-Simons, et dans la limite de constante de couplage faible de Chern-Simons nous avons trouvé que les comportements de la boucle de Wilson et de la boucle de 't Hooft ne changent pas correspondants à une loi périmètre, impliquant qu'il n'y a pas de confinement. De plus, le terme de Chern-Simons ne contribue pas à la boucle de Wilson.

Programmable Self-Assembly: Constructing Global Shape using Biologically-inspire

In this thesis I present a language for instructing a sheet of identically-programmed, flexible, autonomous agents (``cells'') to assemble themselves into a predetermined global shape, using local interactions. The global shape is described as a folding construction on a continuous sheet, using a set of axioms from paper-folding (origami). I provide a means of automatically deriving the cell program, executed by all cells, from the global shape description. With this language, a wide variety of global shapes and patterns can be synthesized, using only local interactions between identically-programmed cells. Examples include flat layered shapes, all plane Euclidean constructions, and a variety of tessellation patterns. In contrast to approaches based on cellular automata or evolution, the cell program is directly derived from the global shape description and is composed from a small number of biologically-inspired primitives: gradients, neighborhood query, polarity inversion, cell-to-cell contact and flexible folding. The cell programs are robust, without relying on regular cell placement, global coordinates, or synchronous operation and can tolerate a small amount of random cell death. I show that an average cell neighborhood of 15 is sufficient to reliably self-assemble complex shapes and geometric patterns on randomly distributed cells. The language provides many insights into the relationship between local and global descriptions of behavior, such as the advantage of constructive languages, mechanisms for achieving global robustness, and mechanisms for achieving scale-independent shapes from a single cell program. The language suggests a mechanism by which many related shapes can be created by the same cell program, in the manner of D'Arcy Thompson's famous coordinate transformations. The thesis illuminates how complex morphology and pattern can emerge from local interactions, and how one can engineer robust self-assembly.

Algorithm for generating defective graphene sheets

An algorithm is presented for the generation of molecular models of defective graphene fragments, containing a majority of 6-membered rings with a small number of 5- and 7-membered rings as defects. The structures are generated from an initial random array of points in 2D space, which are then subject to Delaunay triangulation. The dual of the triangulation forms a Voronoi tessellation of polygons with a range of ring sizes. An iterative cycle of refinement, involving deletion and addition of points followed by further triangulation, is performed until the user-defined criteria for the number of defects are met. The array of points and connectivities are then converted to a molecular structure and subject to geometry optimization using a standard molecular modeling package to generate final atomic coordinates. On the basis of molecular mechanics with minimization, this automated method can generate structures, which conform to user-supplied criteria and avoid the potential bias associated with the manual building of structures. One application of the algorithm is the generation of structures for the evaluation of the reactivity of different defect sites. Ab initio electronic structure calculations on a representative structure indicate preferential fluorination close to 5-ring defects.

Hydrological cycle in the Danube basin in present-day and XXII century simulations by IPCCAR4 global climate models

We present an intercomparison and verification analysis of 20 GCMs (Global Circulation Models) included in the 4th IPCC assessment report regarding their representation of the hydrological cycle on the Danube river basin for 1961–2000 and for the 2161–2200 SRESA1B scenario runs. The basin-scale properties of the hydrological cycle are computed by spatially integrating the precipitation, evaporation, and runoff fields using the Voronoi-Thiessen tessellation formalism. The span of the model- simulated mean annual water balances is of the same order of magnitude of the observed Danube discharge of the Delta; the true value is within the range simulated by the models. Some land components seem to have deficiencies since there are cases of violation of water conservation when annual means are considered. The overall performance and the degree of agreement of the GCMs are comparable to those of the RCMs (Regional Climate Models) analyzed in a previous work, in spite of the much higher resolution and common nesting of the RCMs. The reanalyses are shown to feature several inconsistencies and cannot be used as a verification benchmark for the hydrological cycle in the Danubian region. In the scenario runs, for basically all models the water balance decreases, whereas its interannual variability increases. Changes in the strength of the hydrological cycle are not consistent among models: it is confirmed that capturing the impact of climate change on the hydrological cycle is not an easy task over land areas. Moreover, in several cases we find that qualitatively different behaviors emerge among the models: the ensemble mean does not represent any sort of average model, and often it falls between the models’ clusters.

From symmetry breaking to Poisson Point Process in 2D Voronoi Tessellations: the generic nature of hexagons

We bridge the properties of the regular triangular, square, and hexagonal honeycomb Voronoi tessellations of the plane to the Poisson-Voronoi case, thus analyzing in a common framework symmetry breaking processes and the approach to uniform random distributions of tessellation-generating points. We resort to ensemble simulations of tessellations generated by points whose regular positions are perturbed through a Gaussian noise, whose variance is given by the parameter α2 times the square of the inverse of the average density of points. We analyze the number of sides, the area, and the perimeter of the Voronoi cells. For all valuesα >0, hexagons constitute the most common class of cells, and 2-parameter gamma distributions provide an efficient description of the statistical properties of the analyzed geometrical characteristics. The introduction of noise destroys the triangular and square tessellations, which are structurally unstable, as their topological properties are discontinuous in α = 0. On the contrary, the honeycomb hexagonal tessellation is topologically stable and, experimentally, all Voronoi cells are hexagonal for small but finite noise withα <0.12. For all tessellations and for small values of α, we observe a linear dependence on α of the ensemble mean of the standard deviation of the area and perimeter of the cells. Already for a moderate amount of Gaussian noise (α >0.5), memory of the specific initial unperturbed state is lost, because the statistical properties of the three perturbed regular tessellations are indistinguishable. When α >2, results converge to those of Poisson-Voronoi tessellations. The geometrical properties of n-sided cells change with α until the Poisson- Voronoi limit is reached for α > 2; in this limit the Desch law for perimeters is shown to be not valid and a square root dependence on n is established. This law allows for an easy link to the Lewis law for areas and agrees with exact asymptotic results. Finally, for α >1, the ensemble mean of the cells area and perimeter restricted to the hexagonal cells agree remarkably well with the full ensemble mean; this reinforces the idea that hexagons, beyond their ubiquitous numerical prominence, can be interpreted as typical polygons in 2D Voronoi tessellations.

Symmetry-break in Voronoi tessellations

We analyse in a common framework the properties of the Voronoi tessellations resulting from regular 2D and 3D crystals and those of tessellations generated by Poisson distributions of points, thus joining on symmetry breaking processes and the approach to uniform random distributions of seeds. We perturb crystalline structures in 2D and 3D with a spatial Gaussian noise whose adimensional strength is α and analyse the statistical properties of the cells of the resulting Voronoi tessellations using an ensemble approach. In 2D we consider triangular, square and hexagonal regular lattices, resulting into hexagonal, square and triangular tessellations, respectively. In 3D we consider the simple cubic (SC), body-centred cubic (BCC), and face-centred cubic (FCC) crystals, whose corresponding Voronoi cells are the cube, the truncated octahedron, and the rhombic dodecahedron, respectively. In 2D, for all values α>0, hexagons constitute the most common class of cells. Noise destroys the triangular and square tessellations, which are structurally unstable, as their topological properties are discontinuous in α=0. On the contrary, the honeycomb hexagonal tessellation is topologically stable and, experimentally, all Voronoi cells are hexagonal for small but finite noise with α<0.12. Basically, the same happens in the 3D case, where only the tessellation of the BCC crystal is topologically stable even against noise of small but finite intensity. In both 2D and 3D cases, already for a moderate amount of Gaussian noise (α>0.5), memory of the specific initial unperturbed state is lost, because the statistical properties of the three perturbed regular tessellations are indistinguishable. When α>2, results converge to those of Poisson-Voronoi tessellations. In 2D, while the isoperimetric ratio increases with noise for the perturbed hexagonal tessellation, for the perturbed triangular and square tessellations it is optimised for specific value of noise intensity. The same applies in 3D, where noise degrades the isoperimetric ratio for perturbed FCC and BCC lattices, whereas the opposite holds for perturbed SCC lattices. This allows for formulating a weaker form of the Kelvin conjecture. By analysing jointly the statistical properties of the area and of the volume of the cells, we discover that also the cells shape heavily fluctuates when noise is introduced in the system. In 2D, the geometrical properties of n-sided cells change with α until the Poisson-Voronoi limit is reached for α>2; in this limit the Desch law for perimeters is shown to be not valid and a square root dependence on n is established, which agrees with exact asymptotic results. Anomalous scaling relations are observed between the perimeter and the area in the 2D and between the areas and the volumes of the cells in 3D: except for the hexagonal (2D) and FCC structure (3D), this applies also for infinitesimal noise. In the Poisson-Voronoi limit, the anomalous exponent is about 0.17 in both the 2D and 3D case. A positive anomaly in the scaling indicates that large cells preferentially feature large isoperimetric quotients. As the number of faces is strongly correlated with the sphericity (cells with more faces are bulkier), in 3D it is shown that the anomalous scaling is heavily reduced when we perform power law fits separately on cells with a specific number of faces.

Three-dimensional random Voronoi tessellations: From cubic crystal lattices to Poisson point processes

We perturb the SC, BCC, and FCC crystal structures with a spatial Gaussian noise whose adimensional strength is controlled by the parameter a, and analyze the topological and metrical properties of the resulting Voronoi Tessellations (VT). The topological properties of the VT of the SC and FCC crystals are unstable with respect to the introduction of noise, because the corresponding polyhedra are geometrically degenerate, whereas the tessellation of the BCC crystal is topologically stable even against noise of small but finite intensity. For weak noise, the mean area of the perturbed BCC and FCC crystals VT increases quadratically with a. In the case of perturbed SCC crystals, there is an optimal amount of noise that minimizes the mean area of the cells. Already for a moderate noise (a>0.5), the properties of the three perturbed VT are indistinguishable, and for intense noise (a>2), results converge to the Poisson-VT limit. Notably, 2-parameter gamma distributions are an excellent model for the empirical of of all considered properties. The VT of the perturbed BCC and FCC structures are local maxima for the isoperimetric quotient, which measures the degre of sphericity of the cells, among space filling VT. In the BCC case, this suggests a weaker form of the recentluy disproved Kelvin conjecture. Due to the fluctuations of the shape of the cells, anomalous scalings with exponents >3/2 is observed between the area and the volumes of the cells, and, except for the FCC case, also for a->0. In the Poisson-VT limit, the exponent is about 1.67. As the number of faces is positively correlated with the sphericity of the cells, the anomalous scaling is heavily reduced when we perform powerlaw fits separately on cells with a specific number of faces.

Modelling the reorientation of sea-ice faults as the wind changes direction

A discrete-element model of sea ice is used to study how a 90° change in wind direction alters the pattern of faults generated through mechanical failure of the ice. The sea-ice domain is 400km in size and consists of polygonal floes obtained through a Voronoi tessellation. Initially the floes are frozen together through viscous–elastic joints that can break under sufficient compressive, tensile and shear deformation. A constant wind-stress gradient is applied until the initially frozen ice pack is broken into roughly diamond-shaped aggregates, with crack angles determined by wing-crack formation. Then partial refreezing of the cracks delineating the aggregates is modelled through reduction of their length by a particular fraction, the ice pack deformation is neglected and the wind stress is rotated by 90°. New cracks form, delineating aggregates with a different orientation. Our results show the new crack orientation depends on the refrozen fraction of the initial faults: as this fraction increases, the new cracks gradually rotate to the new wind direction, reaching 90° for fully refrozen faults. Such reorientation is determined by a competition between new cracks forming at a preferential angle determined by the wing-crack theory and at old cracks oriented at a less favourable angle but having higher stresses due to shorter contacts across the joints

Growth and replication : exploring facade subdivision based on natural processes

Generative methods for subdivision of building façades are presented in this thesis through a series of case studies exploring methods of stochastic generation, tiling and tessellation and branching structures.  In each of these studies, a method of generative design based on natural phenomena of growth and replication is described algorithmically.

Biorremoção de corante direto de efluente industrial simulado utilizando levedura liofilizada

One of the most primal ways of human work already known is the tessellation and ginning for the production of fabric and clothing - what used to be, back in those days, statement of power and status. The arrival of the Industrial Revolution - in the middle of the XVIII century at Britain - increased the textile industry production, and what used to be manufactured and hard to obtain, starts then to be produced in mechanical ways and large-scale. Despite all the boost given to the economy of an expanding capitalist market, it should be pointed out the consequences of this major industrialization, especially the environmental ones, more and more concerning nowadays. The emissions of waste - that sometimes could be toxic - in effluents can possibly contaminate the aquatic ecosystems, causing a huge damage to its fauna and flora, affecting therefore all the biodiversity, reaching inclusively the humans. To avoid these problems, a few strategies have been taking place in the attempt to eliminate - or at least reduce - the amount of dye found in the effluents, and as the textile industry constantly leaves waste, efficient methods - that present good results in a short period of time - with a low cost are needed. The present study will test the bioremoval capacity of yeast (Saccharomyces cerevisiae) in contact with dyes in a fix concentration, diluted in water with three different pH values. The tests will be done duplicate, and after the concentration analyses - made by spectrophotometry - it will be analyzed which pH shows major efficiency in the dye removal and what is the influence of the biomass in this process

Mechanical Alterations in airway smooth muscle after interaction with indoor pollutant – A mathematical model.

The viscoelasticity of mammalian lung is determined by the mechanical properties and structural regulation of the airway smooth muscle (ASM). The exposure to polluted air may deteriorate these properties with harmful consequences to individual health. Formaldehyde (FA) is an important indoor pollutant found among volatile organic compounds. This pollutant permeates through the smooth muscle tissue forming covalent bonds between proteins in the extracellular matrix and intracellular protein structure changing mechanical properties of ASM and inducing asthma symptoms, such as airway hyperresponsiveness, even at low concentrations. In the experimental scenario, the mechanical effect of FA is the stiffening of the tissue, but the mechanism behind this effect is not fully understood. Thus, the aim of this study is to reproduce the mechanical behavior of the ASM, such as contraction and stretching, under FA action or not. For this, it was created a two-dimensional viscoelastic network model based on Voronoi tessellation solved using Runge-Kutta method of fourth order. The equilibrium configuration was reached when the forces in different parts of the network were equal. This model simulates the mechanical behavior of ASM through of a network of dashpots and springs. This dashpot-spring mechanical coupling mimics the composition of the actomyosin machinery of ASM through the contraction of springs to a minimum length. We hypothesized that formation of covalent bonds, due to the FA action, can be represented in the model by a simple change in the elastic constant of the springs, while the action of methacholine (MCh) reduce the equilibrium length of the spring. A sigmoid curve of tension as a function of MCh doses was obtained, showing increased tension when the muscle strip was exposed to FA. Our simulations suggest that FA, at a concentration of 0.1 ppm, can affect the elastic properties of the smooth muscle ¯bers by a factor of 120%. We also analyze the dynamic mechanical properties, observing the viscous and elastic behavior of the network. Finally, the proposed model, although simple, incorporates the phenomenology of both MCh and FA and reproduces experimental results observed with in vitro exposure of smooth muscle to FA. Thus, this new mechanical approach incorporates several well know features of the contractile system of the cells in a tissue level model. The model can also be used in different biological scales.

Mechanical alterations in airway smooth muscle after interaction with indoor pollutant - A mathematical model

The viscoelasticity of mammalian lung is determined by the mechanical properties and structural regulation of the airway smooth muscle (ASM). The exposure to polluted air may deteriorate these properties with harmful consequences to individual health. Formaldehyde (FA) is an important indoor pollutant found among volatile organic compounds. This pollutant permeates through the smooth muscle tissue forming covalent bonds between proteins in the extracellular matrix and intracellular protein structure changing mechanical properties of ASM and inducing asthma symptoms, such as airway hyperresponsiveness, even at low concentrations. In the experimental scenario, the mechanical effect of FA is the stiffening of the tissue, but the mechanism behind this effect is not fully w1derstood. Thus, the aim of this study is to reproduce the mechanical behavior of the ASM, such as contraction and stretching, under FA action or not. For this, it was created a two-dimensional viscoelastic network model based on Voronoi tessellation solved using Runge-Kutta method of fourth order. The equilibrium configuration was reached when the forces in different parts of the network were equal. This model simulates the mechanical behavior of ASM through of a network of dashpots and springs. This dashpot-spring mechanical coupling mimics the composition of the actomyosin machinery of ASM through the contraction of springs to a minimum length. We hypothesized that formation of covalent bonds, due to the FA action, can be represented in the model by a simple change in the elastic constant of the springs, while the action of methacholinc (MCh) reduce the equilibrium length of the spring. A sigmoid curve of tension as a function of MCh doses was obtained, showing increased tension when the muscle strip was exposed to FA. Our simulations suggest that FA, at a concentration of 0.1 ppm, can affect the elastic properties of the smooth muscle fibers by a factor of 120%. We also analyze the dynamic mechanical properties, observing the viscous and elastic behavior of the network. Finally, the proposed model, although simple, ir1corporates the phenomenology of both MCh and FA and reproduces experirnental results observed with ir1 vitro exposure of smooth muscle to .FA. Thus, this new mechanical approach incorporates several well know features of the contractile system of the cells ir1 a tissue level model. The model can also be used in different biological scales.