Local congruence of chain complexes

The object of this paper is to transform a set of local chain complexes to a single global complex using an equivalence relation of congruence of cells, solving topologically the numerical inaccuracies of floating-point arithmetics. While computing the space arrangement generated by a collection of cellular complexes, one may start from independently and efficiently computing the intersection of each single input 2-cell with the others. The topology of these intersections is codified within a set of (0-2)-dimensional chain complexes. The target of this paper is to merge the local chains by using the equivalence relations of {\epsilon}-congruence between 0-, 1-, and 2-cells (elementary chains). In particular, we reduce the block-diagonal coboundary matrices [\Delta_0] and [\Delta_1], used as matrix accumulators of the local coboundary chains, to the global matrices [\delta_0] and [\delta_1], representative of congruence topology, i.e., of congruence quotients between all 0-,1-,2-cells, via elementary algebraic operations on their columns. This algorithm is codified using the Julia porting of the SuiteSparse:GraphBLAS implementation of the GraphBLAS standard, conceived to efficiently compute algorithms on large graphs using linear algebra and sparse matrices [1, 2].Comment: to submi

Proto-Plasm: parallel language for adaptive and scalable modelling of biosystems

This paper discusses the design goals and the first developments of Proto-Plasm, a novel computational environment to produce libraries of executable, combinable and customizable computer models of natural and synthetic biosystems, aiming to provide a supporting framework for predictive understanding of structure and behaviour through multiscale geometric modelling and multiphysics simulations. Admittedly, the Proto-Plasm platform is still in its infancy. Its computational framework—language, model library, integrated development environment and parallel engine—intends to provide patient-specific computational modelling and simulation of organs and biosystem, exploiting novel functionalities resulting from the symbolic combination of parametrized models of parts at various scales. Proto-Plasm may define the model equations, but it is currently focused on the symbolic description of model geometry and on the parallel support of simulations. Conversely, CellML and SBML could be viewed as defining the behavioural functions (the model equations) to be used within a Proto-Plasm program. Here we exemplify the basic functionalities of Proto-Plasm, by constructing a schematic heart model. We also discuss multiscale issues with reference to the geometric and physical modelling of neuromuscular junctions

Chain-Based Representations for Solid and Physical Modeling

In this paper we show that the (co)chain complex associated with a decomposition of the computational domain, commonly called a mesh in computational science and engineering, can be represented by a block-bidiagonal matrix that we call the Hasse matrix. Moreover, we show that topology-preserving mesh refinements, produced by the action of (the simplest) Euler operators, can be reduced to multilinear transformations of the Hasse matrix representing the complex. Our main result is a new representation of the (co)chain complex underlying field computations, a representation that provides new insights into the transformations induced by local mesh refinements. Our approach is based on first principles and is general in that it applies to most representational domains that can be characterized as cell complexes, without any restrictions on their type, dimension, codimension, orientability, manifoldness, connectedness

Solid and Physical Modeling with Chain Complexes

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Abstract Solid and Physical Modeling with Chain Complexes

In this paper we show that the (co)chain complex associated with a decomposition of the computational domain, commonly called a mesh in computational science and engineering, can be represented by a block-bidiagonal matrix that we call the Hasse matrix. Moreover, we show that topologypreserving mesh refinements, produced by the action of (the simplest) Euler operators, can be reduced to multi-linear transformations of the Hasse matrix representing the complex. Our main result is a new representation of the (co)chain complex underlying field computations, a representation that provides new insights into the transformations induced by local mesh refinements. This paper is a further contribution towards bridging the subject of computer representations for solid and physical modeling—which flourished border-line between computer graphics, engineering mechanic