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  • An enhanced monarch butterfly optimization with self-adaptive crossover operator for unconstrained and constrained optimization problems
    Nat. Comput. (IF 1.33) Pub Date : 2020-05-21
    Mingyang Chen

    Inspired by the phenomenon of migration of monarch butterflies, Wang et al. developed a novel promising swarm intelligence algorithm, called monarch butterfly optimization (MBO), for addressing unconstrained low-dimensional optimization problems. In this paper, we firstly extend the application area of the basic MBO to solve the constrained optimization problems. At the same time, the crossover operator

    更新日期:2020-05-21
  • Attractor landscapes in Boolean networks with firing memory: a theoretical study applied to genetic networks
    Nat. Comput. (IF 1.33) Pub Date : 2020-05-09
    Eric Goles, Fabiola Lobos, Gonzalo A. Ruz, Sylvain Sené

    In this paper we study the dynamical behavior of Boolean networks with firing memory, namely Boolean networks whose vertices are updated synchronously depending on their proper Boolean local transition functions so that each vertex remains at its firing state a finite number of steps. We prove in particular that these networks have the same computational power than the classical ones, i.e. any Boolean

    更新日期:2020-05-09
  • Search space reduction of asynchrony immune cellular automata
    Nat. Comput. (IF 1.33) Pub Date : 2020-04-27
    Luca Mariot, Luca Manzoni, Alberto Dennunzio

    We continue the study of asynchrony immunity in cellular automata (CA), which can be considered as a generalization of correlation immunity in the case of vectorial Boolean functions. The property could have applications as a countermeasure for side-channel attacks in CA-based cryptographic primitives, such as S-boxes and pseudorandom number generators. We first give some theoretical results on the

    更新日期:2020-04-27
  • The impact of alphabet size on pattern complexity of maxmin- $$\omega$$ω cellular automata
    Nat. Comput. (IF 1.33) Pub Date : 2020-04-14
    Ebrahim L. Patel

    We present an analysis of an additive cellular automaton (CA) under asynchronous dynamics. The asynchronous scheme is maxmin-\(\omega\), a deterministic system, introduced in our previous work with a binary alphabet. Extending this work, we study the impact of a larger alphabet, which also allows a meaningful inference of the behaviour of the resultant CA from the asymptotic behaviour of the maxmin-\(\omega\)

    更新日期:2020-04-23
  • Solving two-dimensional cutting stock problem via a DNA computing algorithm
    Nat. Comput. (IF 1.33) Pub Date : 2020-03-07
    M. Dodge, S. A. MirHassani, F. Hooshmand

    Two-dimensional cutting stock problem (TDCSP) is a well-known combinatorial optimization problem in which a given set of two-dimensional small pieces with different shapes should be cut from a given main board so that the demand of each small piece is satisfied and the total waste is minimized. Since TDCSP is an NP-complete problem, it is unsolvable in polynomial time on electronic computers. However

    更新日期:2020-04-23
  • Concurrency in Boolean networks
    Nat. Comput. (IF 1.33) Pub Date : 2019-06-08
    Thomas Chatain, Stefan Haar, Juraj Kolčák, Loïc Paulevé, Aalok Thakkar

    Boolean networks (BNs) are widely used to model the qualitative dynamics of biological systems. Besides the logical rules determining the evolution of each component with respect to the state of its regulators, the scheduling of component updates can have a dramatic impact on the predicted behaviours. In this paper, we explore the use of Read (contextual) Petri Nets (RPNs) to study dynamics of BNs

    更新日期:2020-04-23
  • Boolean dynamics revisited through feedback interconnections
    Nat. Comput. (IF 1.33) Pub Date : 2018-10-25
    Madalena Chaves, Daniel Figueiredo, Manuel A. Martins

    Boolean models of physical or biological systems describe the global dynamics of the system and their attractors typically represent asymptotic behaviors. In the case of large networks composed of several modules, it may be difficult to identify all the attractors. To explore Boolean dynamics from a novel viewpoint, we will analyse the dynamics emerging from the composition of two known Boolean modules

    更新日期:2020-04-23
  • Maximum sensitivity to update schedules of elementary cellular automata over periodic configurations
    Nat. Comput. (IF 1.33) Pub Date : 2019-07-10
    Kévin Perrot, Marco Montalva-Medel, Pedro P. B. de Oliveira, Eurico L. P. Ruivo

    This work is a thoughtful extension of the ideas sketched in Montalva et al. (AUTOMATA 2017 exploratory papers proceedings, 2017), aiming at classifying elementary cellular automata (ECA) according to their maximal one-step sensitivity to changes in the schedule of cells update. It provides a complete classification of the ECA rule space for all period sizes \(n > 9\) and, together with the classification

    更新日期:2020-04-23
  • About block-parallel Boolean networks: a position paper
    Nat. Comput. (IF 1.33) Pub Date : 2020-01-03
    Jacques Demongeot, Sylvain Sené

    In automata networks, it is well known that the way entities update their states over time has a major impact on their dynamics. In particular, depending on the chosen update schedule, the underlying dynamical systems may exhibit more or less asymptotic dynamical behaviours such as fixed points or limit cycles. Since such mathematical models have been used in the framework of biological networks modelling

    更新日期:2020-04-23
  • Spiking neural networks modelled as timed automata: with parameter learning
    Nat. Comput. (IF 1.33) Pub Date : 2019-01-17
    Elisabetta De Maria, Cinzia Di Giusto, Laetitia Laversa

    In this paper we address the issue of automatically learning parameters of spiking neural networks. Biological neurons are formalized as timed automata and synaptical connections are represented as shared channels among these automata. Such a formalism allows us to take into account several time-related aspects, such as the influence of past inputs in the computation of the potential value of each

    更新日期:2020-04-23
  • Bionic vision system and its application in license plate recognition
    Nat. Comput. (IF 1.33) Pub Date : 2019-06-06
    Zhenjie Yao, Weidong Yi

    Conventional computer vision systems detect object after super-resolution (SR) or image reconstruction of the whole image, which is not an economical manner. By imitating the visual system of human beings, we proposed the bionic vision system (BVS), which is mainly composed by three parts: object detection by visual attention model, object-oriented SR reconstruction and object recognition by convolutional

    更新日期:2020-04-23
  • Reversible causal graph dynamics: invertibility, block representation, vertex-preservation
    Nat. Comput. (IF 1.33) Pub Date : 2019-10-24
    P. Arrighi, S. Martiel, S. Perdrix

    Causal Graph Dynamics extend Cellular Automata to arbitrary time-varying graphs of bounded degree. The whole graph evolves in discrete time steps, and this global evolution is required to have a number of symmetries: shift-invariance (it acts everywhere the same) and causality (information has a bounded speed of propagation). We add a further physics-like symmetry, namely reversibility. In particular

    更新日期:2020-04-23
  • On the influence of the interaction graph on a finite dynamical system
    Nat. Comput. (IF 1.33) Pub Date : 2019-02-13
    Maximilien Gadouleau

    A finite dynamical system (FDS) is a system of multivariate functions over a finite alphabet, that is typically used to model a network of interacting entities. The main feature of a finite dynamical system is its interaction graph, which indicates which local functions depend on which variables; the interaction graph is a qualitative representation of the interactions amongst entities on the network

    更新日期:2020-04-23
  • Approximate majority analyses using tri-molecular chemical reaction networks
    Nat. Comput. (IF 1.33) Pub Date : 2019-08-08
    Anne Condon, Monir Hajiaghayi, David Kirkpatrick, Ján Maňuch

    Approximate Majority is a well-studied problem in the context of chemical reaction networks (CRNs) and their close relatives, population protocols: Given a mixture of two types of species with an initial gap between their counts, a CRN computation must reach consensus on the majority species. Angluin, Aspnes, and Eisenstat proposed a simple population protocol for Approximate Majority and proved correctness

    更新日期:2020-04-23
  • Generation and robustness of Boolean networks to model Clostridium difficile infection
    Nat. Comput. (IF 1.33) Pub Date : 2019-02-14
    Dante Travisany, Eric Goles, Mauricio Latorre, María-Paz Cortés, Alejandro Maass

    One of the more common healthcare associated infection is Chronic diarrhea. This disease is caused by the bacterium Clostridium difficile which alters the normal composition of the human gut flora. The most successful therapy against this infection is the fecal microbial transplant (FMT). They displace C. difficile and contribute to gut microbiome resilience, stability and prevent further episodes

    更新日期:2020-04-23
  • A tutorial on elementary cellular automata with fully asynchronous updating
    Nat. Comput. (IF 1.33) Pub Date : 2020-01-23
    Nazim Fatès

    We present a panorama of the convergence properties of the 256 Elementary Cellular Automata under fully asynchronous updating, that is, when only one cell is updated at each time step. We regroup here various results which have been presented in different articles and expose a full analysis of the behaviour of finite systems with periodic boundary conditions. Our classification relies on the scaling

    更新日期:2020-04-23
  • From electric circuits to chemical networks
    Nat. Comput. (IF 1.33) Pub Date : 2019-09-16
    Luca Cardelli, Mirco Tribastone, Max Tschaikowski

    Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same functionality is useful to biological organisms, where it is implemented by a completely different set of discrete components (typically proteins) and signal representations

    更新日期:2020-04-23
  • A self-adaptive multi-population differential evolution algorithm
    Nat. Comput. (IF 1.33) Pub Date : 2019-08-26
    Lin Zhu, Yongjie Ma, Yulong Bai

    Differential evolution (DE) is an efficient population-based search algorithm for solving numerical optimization problems. However, the performance of DE is very sensitive to the choice of mutation strategies and their associated control parameters. In this paper, we propose a self-adaptive multi-population differential evolution algorithm, called SAMDE. The population is randomly divided into three

    更新日期:2020-04-23
  • On the minimal number of generators of endomorphism monoids of full shifts
    Nat. Comput. (IF 1.33) Pub Date : 2020-02-14
    Alonso Castillo-Ramirez

    For a group G and a finite set A, denote by \(\mathrm{End}(A^G)\) the monoid of all continuous shift commuting self-maps of \(A^G\) and by \(\mathrm{Aut}(A^G)\) its group of units. We study the minimal cardinality of a generating set, known as the rank, of \(\mathrm{End}(A^G)\) and \(\mathrm{Aut}(A^G)\). In the first part, when G is a finite group, we give upper and lower bounds for the rank of \(\mathrm{Aut}(A^G)\)

    更新日期:2020-04-23
  • Perception of cloth in assistive robotic manipulation tasks
    Nat. Comput. (IF 1.33) Pub Date : 2020-02-12
    Pablo Jiménez, Carme Torras

    Assistive robots need to be able to perform a large number of tasks that imply some type of cloth manipulation. These tasks include domestic chores such as laundry handling or bed-making, among others, as well as dressing assistance to disabled users. Due to the deformable nature of fabrics, this manipulation requires a strong perceptual feedback. Common perceptual skills that enable robots to complete

    更新日期:2020-04-23
  • Computing with biological switches and clocks.
    Nat. Comput. Pub Date : 2018-12-14
    Neil Dalchau,Gregory Szép,Rosa Hernansaiz-Ballesteros,Chris P Barnes,Luca Cardelli,Andrew Phillips,Attila Csikász-Nagy

    The complex dynamics of biological systems is primarily driven by molecular interactions that underpin the regulatory networks of cells. These networks typically contain positive and negative feedback loops, which are responsible for switch-like and oscillatory dynamics, respectively. Many computing systems rely on switches and clocks as computational modules. While the combination of such modules

    更新日期:2019-11-01
  • Scaling up genetic circuit design for cellular computing: advances and prospects.
    Nat. Comput. Pub Date : 2018-12-14
    Yiyu Xiang,Neil Dalchau,Baojun Wang

    Synthetic biology aims to engineer and redesign biological systems for useful real-world applications in biomanufacturing, biosensing and biotherapy following a typical design-build-test cycle. Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems. Two types are Boolean logic inspired TRUE or

    更新日期:2019-11-01
  • Rough sets: past, present, and future.
    Nat. Comput. Pub Date : 2018-12-14
    Andrzej Skowron,Soma Dutta

    Introduction of rough sets by Professor Zdzisław Pawlak has completed 35 years. The theory has already attracted the attention of many researchers and practitioners, who have contributed essentially to its development, from all over the world. The methods, developed based on rough set theory alone or in combination with other approaches, found applications in many areas. In this article, we outline

    更新日期:2019-11-01
  • A tutorial on multiobjective optimization: fundamentals and evolutionary methods.
    Nat. Comput. Pub Date : 2018-09-04
    Michael T M Emmerich,André H Deutz

    In almost no other field of computer science, the idea of using bio-inspired search paradigms has been so useful as in solving multiobjective optimization problems. The idea of using a population of search agents that collectively approximate the Pareto front resonates well with processes in natural evolution, immune systems, and swarm intelligence. Methods such as NSGA-II, SPEA2, SMS-EMOA, MOPSO,

    更新日期:2019-11-01
  • Extended spiking neural P systems with white hole rules and their red-green variants.
    Nat. Comput. Pub Date : 2018-05-22
    Artiom Alhazov,Rudolf Freund,Sergiu Ivanov,Marion Oswald,Sergey Verlan

    We consider extended spiking neural P systems with the additional possibility of so-called "white hole rules", which send the complete contents of a neuron to other neurons, and we prove that this extension of the original model can easily simulate register machines. Based on this proof, we then define red-green variants of these extended spiking neural P systems with white hole rules and show how

    更新日期:2019-11-01
  • An all-optical soliton FFT computational arrangement in the 3NLSE-domain.
    Nat. Comput. Pub Date : 2018-05-22
    Anastasios G Bakaoukas

    In this paper an all-optical soliton method for calculating the Fast Fourier Transform (FFT) algorithm is presented. The method comes as an extension of the calculation methods (soliton gates) as they become possible in the cubic non-linear Schrödinger equation (3NLSE) domain, and provides a further proof of the computational abilities of the scheme. The method involves collisions entirely between

    更新日期:2019-11-01
  • Petri-net-based 2D design of DNA walker circuits.
    Nat. Comput. Pub Date : 2018-03-27
    David Gilbert,Monika Heiner,Christian Rohr

    We consider localised DNA computation, where a DNA strand walks along a binary decision graph to compute a binary function. One of the challenges for the design of reliable walker circuits consists in leakage transitions, which occur when a walker jumps into another branch of the decision graph. We automatically identify leakage transitions, which allows for a detailed qualitative and quantitative

    更新日期:2019-11-01
  • Programming discrete distributions with chemical reaction networks.
    Nat. Comput. Pub Date : 2018-03-27
    Luca Cardelli,Marta Kwiatkowska,Luca Laurenti

    We explore the range of probabilistic behaviours that can be engineered with Chemical Reaction Networks (CRNs). We give methods to "program" CRNs so that their steady state is chosen from some desired target distribution that has finite support in [Formula: see text], with [Formula: see text]. Moreover, any distribution with countable infinite support can be approximated with arbitrarily small error

    更新日期:2019-11-01
  • Chemical reaction network designs for asynchronous logic circuits.
    Nat. Comput. Pub Date : 2018-03-27
    Luca Cardelli,Marta Kwiatkowska,Max Whitby

    Chemical reaction networks (CRNs) are a versatile language for describing the dynamical behaviour of chemical kinetics, capable of modelling a variety of digital and analogue processes. While CRN designs for synchronous sequential logic circuits have been proposed and their implementation in DNA demonstrated, a physical realisation of these devices is difficult because of their reliance on a clock

    更新日期:2019-11-01
  • The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics.
    Nat. Comput. Pub Date : 2018-03-27
    Thomas E Ouldridge

    Improved understanding of molecular systems has only emphasised the sophistication of networks within the cell. Simultaneously, the advance of nucleic acid nanotechnology, a platform within which reactions can be exquisitely controlled, has made the development of artificial architectures and devices possible. Vital to this progress has been a solid foundation in the thermodynamics of molecular systems

    更新日期:2019-11-01
  • Design of nucleic acid strands with long low-barrier folding pathways.
    Nat. Comput. Pub Date : 2017-07-12
    Anne Condon,Bonnie Kirkpatrick,Ján Maňuch

    A major goal of natural computing is to design biomolecules, such as nucleic acid sequences, that can be used to perform computations. We design sequences of nucleic acids that are "guaranteed" to have long folding pathways relative to their length. This particular sequences with high probability follow low-barrier folding pathways that visit a large number of distinct structures. Long folding pathways

    更新日期:2019-11-01
  • Dynamic vehicle routing with time windows in theory and practice.
    Nat. Comput. Pub Date : 2017-03-04
    Zhiwei Yang,Jan-Paul van Osta,Barry van Veen,Rick van Krevelen,Richard van Klaveren,Andries Stam,Joost Kok,Thomas Bäck,Michael Emmerich

    The vehicle routing problem is a classical combinatorial optimization problem. This work is about a variant of the vehicle routing problem with dynamically changing orders and time windows. In real-world applications often the demands change during operation time. New orders occur and others are canceled. In this case new schedules need to be generated on-the-fly. Online optimization algorithms for

    更新日期:2019-11-01
  • Modeling biological gradient formation: combining partial differential equations and Petri nets.
    Nat. Comput. Pub Date : 2016-11-25
    Laura M F Bertens,Jetty Kleijn,Sander C Hille,Monika Heiner,Maciej Koutny,Fons J Verbeek

    Both Petri nets and differential equations are important modeling tools for biological processes. In this paper we demonstrate how these two modeling techniques can be combined to describe biological gradient formation. Parameters derived from partial differential equation describing the process of gradient formation are incorporated in an abstract Petri net model. The quantitative aspects of the resulting

    更新日期:2019-11-01
  • Interactive computations: toward risk management in interactive intelligent systems.
    Nat. Comput. Pub Date : 2016-09-13
    Andrzej Skowron,Andrzej Jankowski

    Understanding the nature of interactions is regarded as one of the biggest challenges in projects related to complex adaptive systems. We discuss foundations for interactive computations in interactive intelligent systems (IIS), developed in the Wistech program and used for modeling complex systems. We emphasize the key role of risk management in problem solving by IIS. The considerations are based

    更新日期:2019-11-01
  • Counter machines and crystallographic structures.
    Nat. Comput. Pub Date : 2016-09-13
    N Jonoska,M Krajcevski,G McColm

    One way to depict a crystallographic structure is by a periodic (di)graph, i.e., a graph whose group of automorphisms has a translational subgroup of finite index acting freely on the structure. We establish a relationship between periodic graphs representing crystallographic structures and an infinite hierarchy of intersection languages 𝒟𝒞ℒ d , d = 0, 1, 2, …, within the intersection classes of

    更新日期:2019-11-01
  • Knowledge representation of motor activity of patients with Parkinson's disease.
    Nat. Comput. Pub Date : 2015-11-28
    Bożena Kostek,Adam Kupryjanow,Andrzej Czyżewski

    An approach to the knowledge representation extraction from biomedical signals analysis concerning motor activity of Parkinson disease patients is proposed in this paper. This is done utilizing accelerometers attached to their body as well as exploiting video image of their hand movements. Experiments are carried out employing artificial neural networks and support vector machine to the recognition

    更新日期:2019-11-01
  • Granular computing in mosaicing of images from capsule endoscopy.
    Nat. Comput. Pub Date : 2015-11-28
    Lukasz Maciura,Jan G Bazan

    This article introduces methods for modeling compound granules used in algorithms which could successfully construct a mosaic from the images coming from an endoscope capsule. In order to apply the algorithm, combined images must have a common area where the correspondence of points is determined. That allows to determine the transformation parameters to compensate movement of the capsule that occurs

    更新日期:2019-11-01
  • Logic circuits from zero forcing.
    Nat. Comput. Pub Date : 2015-08-25
    Daniel Burgarth,Vittorio Giovannetti,Leslie Hogben,Simone Severini,Michael Young

    We design logic circuits based on the notion of zero forcing on graphs; each gate of the circuits is a gadget in which zero forcing is performed. We show that such circuits can evaluate every monotone Boolean function. By using two vertices to encode each logical bit, we obtain universal computation. We also highlight a phenomenon of "back forcing" as a property of each function. Such a phenomenon

    更新日期:2019-11-01
  • Topology driven modeling: the IS metaphor.
    Nat. Comput. Pub Date : 2015-08-25
    Emanuela Merelli,Marco Pettini,Mario Rasetti

    In order to define a new method for analyzing the immune system within the realm of Big Data, we bear on the metaphor provided by an extension of Parisi's model, based on a mean field approach. The novelty is the multilinearity of the couplings in the configurational variables. This peculiarity allows us to compare the partition function [Formula: see text] with a particular functor of topological

    更新日期:2019-11-01
  • A hybrid method for inversion of 3D DC resistivity logging measurements.
    Nat. Comput. Pub Date : 2015-08-25
    Ewa Gajda-Zagórska,Robert Schaefer,Maciej Smołka,Maciej Paszyński,David Pardo

    This paper focuses on the application of hp hierarchic genetic strategy (hp-HGS) for solution of a challenging problem, the inversion of 3D direct current (DC) resistivity logging measurements. The problem under consideration has been formulated as the global optimization one, for which the objective function (misfit between computed and reference data) exhibits multiple minima. In this paper, we consider

    更新日期:2019-11-01
  • Utilising a simulation platform to understand the effect of domain model assumptions.
    Nat. Comput. Pub Date : 2015-02-28
    Kieran Alden,Paul S Andrews,Henrique Veiga-Fernandes,Jon Timmis,Mark Coles

    Computational and mathematical modelling approaches are increasingly being adopted in attempts to further our understanding of complex biological systems. This approach can be subjected to strong criticism as substantial aspects of the biological system being captured are not currently known, meaning assumptions need to be made that could have a critical impact on simulation response. We have utilised

    更新日期:2019-11-01
  • Understanding self-organized regularities in healthcare services based on autonomy oriented modeling.
    Nat. Comput. Pub Date : 2015-02-28
    Li Tao,Jiming Liu

    Self-organized regularities in terms of patient arrivals and wait times have been discovered in real-world healthcare services. What remains to be a challenge is how to characterize those regularities by taking into account the underlying patients' or hospitals' behaviors with respect to various impact factors. This paper presents a case study to address such a challenge. Specifically, it models and

    更新日期:2019-11-01
  • Modeling Scalable Pattern Generation in DNA Reaction Networks.
    Nat. Comput. Pub Date : 2014-12-17
    Peter B Allen,Xi Chen,Zack B Simpson,Andrew D Ellington

    We have developed a theoretical framework for developing patterns in multiple dimensions using controllable diffusion and designed reactions implemented in DNA. This includes so-called strand displacement reactions in which one single-stranded DNA hybridizes to a hemi-duplex DNA and displaces another single-stranded DNA, reversibly or irreversibly. These reactions can be designed to proceed with designed

    更新日期:2019-11-01
  • Reachability bounds for chemical reaction networks and strand displacement systems.
    Nat. Comput. Pub Date : 2014-11-18
    Anne Condon,Bonnie Kirkpatrick,Ján Maňuch

    Chemical reaction networks (CRNs) and DNA strand displacement systems (DSDs) are widely-studied and useful models of molecular programming. However, in order for some DSDs in the literature to behave in an expected manner, the initial number of copies of some reagents is required to be fixed. In this paper we show that, when multiple copies of all initial molecules are present, general types of CRNs

    更新日期:2019-11-01
  • Quantum Cryptography II: How to re-use a one-time pad safely even if P=NP.
    Nat. Comput. Pub Date : 2014-11-18
    Charles H Bennett,Gilles Brassard,Seth Breidbart

    When elementary quantum systems, such as polarized photons, are used to transmit digital information, the uncertainty principle gives rise to novel cryptographic phenomena unachievable with traditional transmission media, e.g. a communications channel on which it is impossible in principle to eavesdrop without a high probability of being detected. With such a channel, a one-time pad can safely be reused

    更新日期:2019-11-01
  • Amorphous computing: examples, mathematics and theory.
    Nat. Comput. Pub Date : 2013-08-16
    W Richard Stark

    The cellular automata model was described by John von Neumann and his friends in the 1950s as a representation of information processing in multicellular tissue. With crystalline arrays of cells and synchronous activity, it missed the mark (Stark and Hughes, BioSystems 55:107-117, 2000). Recently, amorphous computing, a valid model for morphogenesis in multicellular information processing, has begun

    更新日期:2019-11-01
  • Hierarchical Self Assembly of Patterns from the Robinson Tilings: DNA Tile Design in an Enhanced Tile Assembly Model.
    Nat. Comput. Pub Date : 2012-12-12
    Jennifer E Padilla,Wenyan Liu,Nadrian C Seeman

    We introduce a hierarchical self assembly algorithm that produces the quasiperiodic patterns found in the Robinson tilings and suggest a practical implementation of this algorithm using DNA origami tiles. We modify the abstract Tile Assembly Model, (aTAM), to include active signaling and glue activation in response to signals to coordinate the hierarchical assembly of Robinson patterns of arbitrary

    更新日期:2019-11-01
  • Evolutionary mechanics: new engineering principles for the emergence of flexibility in a dynamic and uncertain world.
    Nat. Comput. Pub Date : 2012-09-11
    James M Whitacre,Philipp Rohlfshagen,Axel Bender,Xin Yao

    Engineered systems are designed to deftly operate under predetermined conditions yet are notoriously fragile when unexpected perturbations arise. In contrast, biological systems operate in a highly flexible manner; learn quickly adequate responses to novel conditions, and evolve new routines and traits to remain competitive under persistent environmental change. A recent theory on the origins of biological

    更新日期:2019-11-01
  • Self assembly of rectangular shapes on concentration programming and probabilistic tile assembly models.
    Nat. Comput. Pub Date : 2012-06-01
    Vamsi Kundeti,Sanguthevar Rajasekaran

    Efficient tile sets for self assembling rectilinear shapes is of critical importance in algorithmic self assembly. A lower bound on the tile complexity of any deterministic self assembly system for an n × n square is [Formula: see text] (inferred from the Kolmogrov complexity). Deterministic self assembly systems with an optimal tile complexity have been designed for squares and related shapes in the

    更新日期:2019-11-01
  • Deterministic Function Computation with Chemical Reaction Networks.
    Nat. Comput. Pub Date : 2012-01-01
    Ho-Lin Chen,David Doty,David Soloveichik

    Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology, CRNs are a promising language for the design of artificial molecular control circuitry. Nonetheless, despite the widespread use of CRNs in the natural sciences

    更新日期:2019-11-01
  • Padlock probe-mediated qRT-PCR for DNA computing answer determination.
    Nat. Comput. Pub Date : 2011-06-22
    Fusheng Xiong,Wayne D Frasch

    Padlock probe-mediated quantitative real time PCR (PLP-qRT-PCR) was adapted to quantify the abundance of sequential 10mer DNA sequences for use in DNA computing to identify optimal answers of traveling salesman problems. The protocol involves: (i) hybridization of a linear PLP with a target DNA sequence; (ii) PLP circularization through enzymatic ligation; and (iii) qRT-PCR amplification of the circularized

    更新日期:2019-11-01
  • When to use bit-wise neutrality.
    Nat. Comput. Pub Date : 2011-04-09
    Tobias Friedrich,Frank Neumann

    Representation techniques are important issues when designing successful evolutionary algorithms. Within this field the use of neutrality plays an important role. We examine the use of bit-wise neutrality introduced by Poli and López (2007) from a theoretical point of view and show that this mechanism only enhances mutation-based evolutionary algorithms if not the same number of genotypic bits for

    更新日期:2019-11-01
  • Algorithms on ensemble quantum computers.
    Nat. Comput. Pub Date : 2011-04-09
    P Oscar Boykin,Tal Mor,Vwani Roychowdhury,Farrokh Vatan

    In ensemble (or bulk) quantum computation, all computations are performed on an ensemble of computers rather than on a single computer. Measurements of qubits in an individual computer cannot be performed; instead, only expectation values (over the complete ensemble of computers) can be measured. As a result of this limitation on the model of computation, many algorithms cannot be processed directly

    更新日期:2019-11-01
  • TRANSDUCER GENERATED ARRAYS OF ROBOTIC NANO-ARMS.
    Nat. Comput. Pub Date : 2010-06-01
    Egor Dolzhenko,Nataša Jonoska,Nadrian C Seeman

    We consider sets of two-dimensional arrays, called here transducer generated languages, obtained by iterative applications of transducers (finite state automata with output). Each transducer generates a set of blocks of symbols such that the bottom row of a block is an input string accepted by the transducer and, by iterative application of the transducer, each row of the block is an output of the

    更新日期:2019-11-01
  • Multiplying with DNA.
    Nat. Comput. Pub Date : 2006-11-01
    Gang Wu,Nadrian C Seeman

    A functional machine is not only an assembly of parts, but also an assembly of processes. The processing of each part must obey laws that respect to the property of this part. For example, building any kind of computer entails selecting appropriate components and assembling their properties to function in computation. Here, we describe computation using a DNA strand as the basic unit and we have used

    更新日期:2019-11-01
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