Topology of Cell-Aggregated Planar Graphs

We present new algorithm for growth of non-clustered planar graphs by aggregation of cells with given distribution of size and constraint of connectivity k=3 per node. The emergent graph structures are controlled by two parameters--chemical potential of the cell aggregation and the width of the cell size distribution. We compute several statistical properties of these graphs--fractal dimension of the perimeter, distribution of shortest paths between pairs of nodes and topological betweenness of nodes and links. We show how these topological properties depend on the control parameters of the aggregation process and discuss their relevance for the conduction of current in self-assembled nanopatterns.Comment: 8 pages, 5 figure

Transport Processes on Homogeneous Planar Graphs with Scale-Free Loops

We consider the role of network geometry in two types of diffusion processes: transport of constant-density information packets with queuing on nodes, and constant voltage-driven tunneling of electrons. The underlying network is a homogeneous graph with scale-free distribution of loops, which is constrained to a planar geometry and fixed node connectivity $k=3$. We determine properties of noise, flow and return-times statistics for both processes on this graph and relate the observed differences to the microscopic process details. Our main findings are: (i) Through the local interaction between packets queuing at the same node, long-range correlations build up in traffic streams, which are practically absent in the case of electron transport; (ii) Noise fluctuations in the number of packets and in the number of tunnelings recorded at each node appear to obey the scaling laws in two distinct universality classes; (iii) The topological inhomogeneity of betweenness plays the key role in the occurrence of broad distributions of return times and in the dynamic flow. The maximum-flow spanning trees are characteristic for each process type.Comment: 14 pages, 5 figure

Novel hollow all-carbon structures

A new family of cavernous all-carbon structures is proposed. These molecular cage structures are constructed by edge subdivisions and leapfrog transformations from cubic polyhedra or their duals. The obtained structures were then optimized at the density functional level. These hollow carbon structures represent a new class of carbon allotropes which could lead to many interesting applications.Peer reviewe

On eccentricity-based topological indices study of a class of porphyrin-cored dendrimers

It is revealed from the previous studies that there is a strong relation between the chemical characteristic of a chemical compound and its molecular structure. Topological indices defined on the molecular structure of biomolecules can help to gain a better understanding of their physical features and biological activities. Eccentricity connectivity indices are distance-based molecular structure descriptors that have been used for the mathematical modeling of biological activities of diverse nature. As the porphyrin has photofunctional properties, such as a large absorption cross-section, fluorescence emission, and photosensitizing properties, due to these properties, porphyrin dendrimers can be used as photofunctional nanodevices. In this paper, we compute the exact formulae of different versions of eccentric connectivity index and their corresponding polynomials for a class of porphyrin-cored dendrimers. The results obtained can be used in computer-aided molecular design methods applied to pharmaceutical engineering

Elementary fractal geometry. Networks and carpets involving irrational rotations

Self-similar sets with open set condition, the linear objects of fractal geometry, have been considered mainly for crystallographic data. Here we introduce new symmetry classes in the plane, based on rotation by irrational angles. Examples without characteristic directions, with strong connectedness and small complexity were found in a computer-assisted search. They are surprising since the rotations are given by rational matrices, and the proof of the open set condition usually requires integer data. We develop a classification of self-similar sets by symmetry class and algebraic numbers. Examples are given for various quadratic number fields. .Comment: 29 pages, 12 figure

Towards a combinatorial algorithm for the enumeration of isotopy classes of symmetric cellular embeddings of graphs on hyperbolic surfaces

Based on the recent mathematical theory of isotopic tilings, we present the, to the best of our knowledge, first algorithm for the enumeration of isotopy classes of cellular embeddings of graphs invariant under a given symmetry group on hyperbolic surfaces. To achieve this, we substitute the isotopy classes with combinatorial objects and propose different techniques, guided by structural results on the mapping class group of an orbifold and notions from computational group theory that ensure that the algorithm is computationally tractable. Furthermore, we extend data structures of combinatorial tiling theory to isotopy classes that lead to an actual implementation of the algorithm for symmetry groups generated by rotations. \\From the enumerated combinatorial objects, we produce a range of simple graphs on hyperbolic surfaces represented as symmetric tilings in the hyperbolic plane, illustrating the enumeration with examples and experimentally demonstrating the feasibility of the approach. These tilings are finally projected onto a family of triply-periodic surfaces that are relevant for the natural sciences

Two essays in computational optimization: computing the clar number in fullerene graphs and distributing the errors in iterative interior point methods

Fullerene are cage-like hollow carbon molecules graph of pseudospherical sym- metry consisting of only pentagons and hexagons faces. It has been the object of interest for chemists and mathematicians due to its widespread application in various fields, namely including electronic and optic engineering, medical sci- ence and biotechnology. A Fullerene molecular, Γ n of n atoms has a multiplicity of isomers which increases as N iso ∼ O(n 9 ). For instance, Γ 180 has 79,538,751 isomers. The Fries and Clar numbers are stability predictors of a Fullerene molecule. These number can be computed by solving a (possibly N P -hard) combinatorial optimization problem. We propose several ILP formulation of such a problem each yielding a solution algorithm that provides the exact value of the Fries and Clar numbers. We compare the performances of the algorithm derived from the proposed ILP formulations. One of this algorithm is used to find the Clar isomers, i.e., those for which the Clar number is maximum among all isomers having a given size. We repeated this computational experiment for all sizes up to 204 atoms. In the course of the study a total of 2 649 413 774 isomers were analyzed.The second essay concerns developing an iterative primal dual infeasible path following (PDIPF) interior point (IP) algorithm for separable convex quadratic minimum cost flow network problem. In each iteration of PDIPF algorithm, the main computational effort is solving the underlying Newton search direction system. We concentrated on finding the solution of the corresponding linear system iteratively and inexactly. We assumed that all the involved inequalities can be solved inexactly and to this purpose, we focused on different approaches for distributing the error generated by iterative linear solvers such that the convergences of the PDIPF algorithm are guaranteed. As a result, we achieved theoretical bases that open the path to further interesting practical investiga- tion