On the Concepts of Parallelism in Biomolecular Computing

In this paper we consider DNA and membrane computing, both as theoretical models and as problem solving devices. The basic motivation behind these models of natural computing is using parallelism to make hard problems tractable. In this paper we analyze the concept of parallelism. We will show that parallelism has very different meanings in these models.We introduce the terms ’or-parallelism’ and ’and-parallelism’ for these two basic types of parallelism

Computational network design from functional specifications

Connectivity and layout of underlying networks largely determine agent behavior and usage in many environments. For example, transportation networks determine the flow of traffic in a neighborhood, whereas building floorplans determine the flow of people in a workspace. Designing such networks from scratch is challenging as even local network changes can have large global effects. We investigate how to computationally create networks starting from only high-level functional specifications. Such specifications can be in the form of network density, travel time versus network length, traffic type, destination location, etc. We propose an integer programming-based approach that guarantees that the resultant networks are valid by fulfilling all the specified hard constraints and that they score favorably in terms of the objective function. We evaluate our algorithm in two different design settings, street layout and floorplans to demonstrate that diverse networks can emerge purely from high-level functional specifications

Extensive Gene Remodeling in the Viral World: New Evidence for Nongradual Evolution in the Mobilome Network

International audienceComplex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth

Finite Models of Splicing and Their Complexity

Durante las dos últimas décadas ha surgido una colaboración estrecha entre informáticos, bioquímicos y biólogos moleculares, que ha dado lugar a la investigación en un área conocida como la computación biomolecular. El trabajo en esta tesis pertenece a este área, y estudia un modelo de cómputo llamado sistema de empalme (splicing system). El empalme es el modelo formal del corte y de la recombinación de las moléculas de ADN bajo la influencia de las enzimas de la restricción.Esta tesis presenta el trabajo original en el campo de los sistemas de empalme, que, como ya indica el título, se puede dividir en dos partes. La primera parte introduce y estudia nuevos modelos finitos de empalme. La segunda investiga aspectos de complejidad (tanto computacional como descripcional) de los sistema de empalme. La principal contribución de la primera parte es que pone en duda la asunción general que una definición finita, más realista de sistemas de empalme es necesariamente débil desde un punto de vista computacional. Estudiamos varios modelos alternativos y demostramos que en muchos casos tienen más poder computacional. La segunda parte de la tesis explora otro territorio. El modelo de empalme se ha estudiado mucho respecto a su poder computacional, pero las consideraciones de complejidad no se han tratado apenas. Introducimos una noción de la complejidad temporal y espacial para los sistemas de empalme. Estas definiciones son utilizadas para definir y para caracterizar las clases de complejidad para los sistemas de empalme. Entre otros resultados, presentamos unas caracterizaciones exactas de las clases de empalme en términos de clases de máquina de Turing conocidas. Después, usando una nueva variante de sistemas de empalme, que acepta lenguajes en lugar de generarlos, demostramos que los sistemas de empalme se pueden usar para resolver problemas. Por último, definimos medidas de complejidad descriptional para los sistemas de empalme. Demostramos que en este respecto los sistemas de empalme finitos tienen buenas propiedades comparadosOver the last two decades, a tight collaboration has emerged between computer scientists, biochemists and molecular biologists, which has spurred research into an area known as DNAComputing (also biomolecular computing). The work in this thesis belongs to this field, and studies a computational model called splicing system. Splicing is the formal model of the cutting and recombination of DNA molecules under the influence of restriction enzymes.This thesis presents original work in the field of splicing systems, which, as the title already indicates, can be roughly divided into two parts: 'Finite models of splicing' on the onehand and 'their complexity' on the other. The main contribution of the first part is that it challenges the general assumption that a finite, more realistic definition of splicing is necessarily weal from a computational point of view. We propose and study various alternative models and show that in most cases they have more computational power, often reaching computational completeness. The second part explores other territory. Splicing research has been mainly focused on computational power, but complexity considerations have hardly been addressed. Here we introduce notions of time and space complexity for splicing systems. These definitions are used to characterize splicing complexity classes in terms of well known Turing machine classes. Then, using a new accepting variant of splicing systems, we show that they can also be used as problem solvers. Finally, we study descriptional complexity. We define measures of descriptional complexity for splicing systems and show that for representing regular languages they have good properties with respect to finite automata, especially in the accepting variant

Advanced Computational Engineering

The finite element method is the established simulation tool for the numerical solution of partial differential equations in many engineering problems with many mathematical developments such as mixed finite element methods (FEMs) and other nonstandard FEMs like least-squares, nonconforming, and discontinuous Galerkin (dG) FEMs. Various aspects on this plus related topics ranging from order-reduction methods to isogeometric analysis has been discussed amongst the pariticpants form mathematics and engineering for a large range of applications

Automated Segmentation for Connectomics Utilizing Higher-Order Biological Priors

This thesis presents novel methodological approaches for the automated segmentation of neurons from electron microscopic image volumes using machine learning techniques. New potentials for neural segmentation are revealed by incorporating (high-level) biological prior knowledge. This goes beyond the modeling of neural tissue which has been applied for the purpose of its segmentation, so far. Firstly, the V-Multicut algorithm is introduced which enables the consideration of topological constraints for segmented membranes. In this way, biologically implausible appearances of membranes are corrected. Secondly, this thesis proves that, in addition to local evidence and topological requirements for the detection of neural membranes, the consideration of high-level biological prior knowledge is beneficial. For this task, both the recently proposed Asymmetric Multiway Cut and the introduced Semantic Agglomerative Clustering algorithm are implemented and quantitatively evaluated. To be precise, the spatial separation of dendrites and axons in mammals is exploited to significantly improve the segmentation quality. Additionally, new ways to improve the scalability of the used algorithms are presented. All in all this thesis serves as another step towards fully automated segmentation of neurons and contributes to the field of connectomics

A Survey of Surveillance: Reworking the Male Gaze and the Surveillance Gaze Through Art and Technology

Senior Project submitted to The Division of Arts of Bard College

Formal Verification of P Systems

Membrane systems, also known as P systems, constitute an innovative computational paradigm inspired by the structure and dynamics of the living cell. A P system consists of a hierarchical arrangement of compartments and a finite set of multiset rewriting and communication rules, which operate in a maximally parallel manner. The organic vision of concurrent dynamics captured by membrane systems stands in antithesis with conventional formal modelling methods which focus on algebraic descriptions of distributed systems. As a consequence, verifying such models in a mathematically rigorous way is often elusive and indeed counter-intuitive when considering established approaches, which generally require sequential process representations or highly abstract theoretical frameworks. The prevalent investigations with this objective in the field of membrane computing are ambivalent and inconclusive in the wider application scope of P systems. In this thesis we directly address the formal verification of membrane systems by means of model checking. A fundamental distinction between the agnostic perspective on parallelism, advocated by process calculi, and P systems' emblematic maximally parallel execution strategy is identified. On this basis, we establish that an intuitional translation to traditional process models is inadequate for the purpose of formal verification, due to a state space growth disparity. The observation is essential for this research project: on one hand it implies the feasibility of model checking P systems, and on the other hand it underlines the suitability of this formal verification technique in the context of membrane computing. Model checking entails an exhaustive state space exploration and does not derive inferences based on the independent instructions comprising a state transition. In this respect, we define a new sequential modelling strategy which is optimal for membrane systems and targets the SPIN formal verification tool. We introduce elementary P systems, a distributed computational model which subsumes the feature diversity of the membrane computing paradigm and distils its functional vocabulary. A suite of supporting software tools which gravitate around this formalism has also been developed, comprising of 1. the eps modelling language for elementary P systems; 2. a parser for the eps specification; 3. a model simulator and 4. a translation tool which targets the Promela specification of the SPIN model checker. The formal verification approach proposed in this thesis is progressively demonstrated in four heterogeneous case studies, featuring 1. a parallel algorithm applicable to a structured model; 2. a linear time solution to an NP-complete problem; 3. an innovative implementation of the Dining Philosophers scenario (a synchronisation problem) using an elementary P system and 4. a quantitative analysis of a simple random process implemented without the support of a probabilistic model