Andre R. O. Cavalcanti

Bio: Andre R. O. Cavalcanti is an academic researcher. The author has an hindex of 1, co-authored 1 publications receiving 78 citations.

Computation in Living Cells: Gene Assembly in Ciliates

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An estimation of the number of cells in the human body

Abstract: Background: All living organisms are made of individual and identifiable cells, whose number, together with their size and type, ultimately defines the structure and functions of an organism. While...

The many facets of natural computing

Abstract: Natural computing is the field of research that investigates models and computational techniques inspired by nature and, dually, attempts to understand the world around us in terms of information processing. It is a highly interdisciplinary field that connects the natural sciences with computing science, both at the level of information technology and at the level of fundamental research, [98]. As a matter of fact, natural computing areas and topics come in many flavours, including pure theoretical research, algorithms and software applications, as well as biology, chemistry and physics experimental laboratory research. In this review we describe computing paradigms abstracted from natural phenomena as diverse as self-reproduction, the functioning of the brain, Darwinian evolution, group behaviour, the immune system, the characteristics of life, cell membranes, and morphogenesis. These paradigms can be implemented either on traditional electronic hardware or on alternative physical media such as biomolecular (DNA, RNA) computing, or trapped-ion quantum computing devices. Dually, we describe several natural processes that can be viewed as information processing, such as gene regulatory networks, protein-protein interaction networks, biological transport networks, and gene assembly in unicellular organisms. In the same vein, we list efforts to understand biological systems by engineering semi-synthetic organisms, and to understand the universe from the point of view of information processing. This review was written with the expectation that the reader is a computer scientist with limited knowledge of natural sciences, and it avoids dwelling on the minute details of

Material-based design computation

Abstract: The institutionalized separation between form, structure and material, deeply embedded in modernist design theory, paralleled by a methodological partitioning between modeling, analysis and fabrication, resulted in geometric-driven form generation. Such prioritization of form over material was carried into the development and design logic of CAD. Today, under the imperatives and growing recognition of the failures and environmental liabilities of this approach, modern design culture is experiencing a shift to material aware design. Inspired by Nature’s strategies where form generation is driven by maximal performance with minimal resources through local material property variation, the research reviews, proposes and develops models and processes for a material-based approach in computationally enabled form-generation. Material-based Design Computation is developed and proposed as a set of computational strategies supporting the integration of form, material and structure by incorporating physical form-finding strategies with digital analysis and fabrication. In this approach, material precedes shape, and it is the structuring of material properties as a function of structural and environmental performance that generates design form. The thesis proposes a unique approach to computationally-enabled form-finding procedures, and experimentally investigates how such processes contribute to novel ways of creating, distributing and depositing material forms. Variable Property Design is investigated as a theoretical and technical framework by which to model, analyze and fabricate objects with graduated properties designed to correspond to multiple and continuously varied functional constraints. The following methods were developed as the enabling mechanisms of Material Computation: Tiling Behavior & Digital Anisotropy, Finite Element Synthesis, and Material Pixels. In order to implement this approach as a fabrication process, a novel fabrication technology, termed Variable Property Rapid Prototyping has been developed, designed and patented. Among the potential contributions is the achievement of a high degree of customization through material heterogeneity as compared to conventional design of components and assemblies. Experimental designs employing suggested theoretical and technical frameworks, methods and techniques are presented, discussed and demonstrated. They support product customization, rapid augmentation and variable property fabrication. Developed as approximations of natural formation processes, these design experiments demonstrate the contribution and the potential future of a new design and research field. Thesis Supervisor: William J. Mitchell Title: Alexander Dreyfoos Professor of Architecture and Media Arts and Sciences Department of Architecture, MIT

Models of natural computation : gene assembly and membrane systems

Abstract: This thesis is concerned with two research areas in natural computing: the computational nature of gene assembly and membrane computing. Gene assembly is a process occurring in unicellular organisms called ciliates. During this process genes are transformed through cut-and-paste operations. We study this process from a theoretical point of view. More specifically, we relate the theory of gene assembly to sorting by reversal, which is another well-known theory of DNA transformation. In this way we obtain a novel graph-theoretical representation that provides new insights into the nature of gene assembly. Membrane computing is a computational model inspired by the functioning of membranes in cells. Membrane systems compute in a parallel fashion by moving objects, through membranes, between compartments. We study the computational power of various classes of membrane systems, and also relate them to other well-known models of computation.

The group structure of pivot and loop complementation on graphs and set systems

Abstract: We study the interplay between the principal pivot transform (pivot) and loop complementation for graphs. This is done by generalizing loop complementation (in addition to pivot) to set systems. We show that the operations together, when restricted to single vertices, form the permutation group S 3 . This leads, e.g., to a normal form for sequences of pivots and loop complementation on graphs. The results have consequences for the operations of local complementation and edge complementation on simple graphs: an alternative proof of a classic result involving local and edge complementation is obtained, and the effect of sequences of local complementations on simple graphs is characterized.