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The effect of encapsulation on molecular computing efficiency

The effect of encapsulation on molecular computing efficienc...

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2011 Functional Optical Imaging, FOI 2011

作者： Chaplin, Jack C. Krasnogor, Natalio Russell, Noah A. Neurophotonics Lab. Institute of Biophysics Imaging and Optical Science University of Nottingham Nottingham United Kingdom Interdisciplinary Computing and Complex Systems Group Computer Science University of Nottingham Nottingham United Kingdom

ISBN: (纸本)9781467304511

Research into molecular computation offers exciting possibilities for interfacing computation with biological systems. This could be achieved using light to switch photochromic molecules between states. For example, 6-Nitro-BIPS can be switched from a Spiropyran (SP) state to a Trans-Merocyanine (MC) state using UV photons while visible light switches from MC to SP. The MC state is also fluorescent. Modified spiropyrans targeted to proteins can improve imaging contrast, alter enzyme activity, alter protein interactions and switch vesicle permeability. © 2011 IEEE.

关键词： Enzyme activity

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The effect of encapsulation on molecular computing efficiency

The effect of encapsulation on molecular computing efficienc...

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Functional Optical Imaging (FOI)

作者： Jack C. Chaplin Natalio Krasnogor Noah A. Russell University of Nottingham Nottingham Nottinghamshire GB Interdisciplinary Computing & Complex Systems Group Computer Science University of Nottingham Nottingham UK Neurophotonics Laboratory Institute of Biophysics Imaging and Optical Science University of Nottingham Nottingham UK

Summary Form Only Given. Research into molecular computation offers exciting possibilities for interfacing computation with biological systems. This could be achieved using light to switch photochromic molecules between states. For example, 6-Nitro-BIPS can be switched from a Spiropyran (SP) state to a Trans- Merocyanine (MC) state using UV photons while visible light switches from MC to SP. The MC state is also fluorescent. Modified spiropyrans targeted to proteins can improve imaging contrast, alter enzyme activity, alter protein interactions and switch vesicle permeability. We have used NBIPS to produce data registers and logic gates. NBIPS was encapsulated in silicone rubber (4mM NBIPS in methanol mixed 1:5 with PDMS). Molecules were switched with LEDs while detecting fluorescence with a photodiode. Integer data is stored as the relative concentration of MC molecules in a sample. The register value is determined from the fluorescence and its capacity is limited by the dynamic range. Using ~0. lmW/mm -2 illumination we have implemented a 6-bit register. In the same sample we have also implemented several universal logic gate sets; using light-pulse sequences as inputs and the fluorescent signal as output. The switching quantum efficiency (Φ) is strongly dependent on the immediate chemical environment of the NBIPS molecules. For example, in ethanol Φ SP→MC ~0.17 8 , however, when NBIPS was encapsulated in PDMS we measured the Φ SP→MC to be ~0.017. Although this proof-of-concept system demonstrates the possibility of embedding computation into biological systems, it highlights the importance of controlling the chemical environment to achieve high computational speeds.

关键词： Optical switches Fluorescence Registers Logic gates Lighting Imaging

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A parameter-adaptive dynamic programming approach for inferring cophylogenies

A parameter-adaptive dynamic programming approach for inferr...

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8th Asia-Pacific Bioinformatics Conference, APBC 2010

作者： Merkle, Daniel Middendorf, Martin Wieseke, Nicolas Department of Mathematics and Computer Science University of Southern Denmark Odense Denmark Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Germany

Background: Coevolutionary systems like hosts and their parasites are commonly used model systems for evolutionary studies. Inferring the coevolutionary history based on given phylogenies of both groups is often done by employing a set of possible types of events that happened during coevolution. Costs are assigned to the different types of events and a reconstruction of the common history with a minimal sum of event costs is sought. Results: This paper introduces a new algorithm and a corresponding tool called CoRe-PA, that can be used to infer the common history of coevolutionary systems. The proposed method utilizes an event-based concept for reconciliation analyses where the possible events are cospeciations, sortings, duplications, and (host) switches. All known event-based approaches so far assign costs to each type of cophylogenetic events in order to find a cost-minimal reconstruction. CoRe-PA uses a new parameter-adaptive approach, i.e., no costs have to be assigned to the coevolutionary events in advance. Several biological coevolutionary systems that have already been studied intensely in literature are used to show the performance of CoRe-PA. Conclusion: From a biological point of view reasonable cost values for event-based reconciliations can often be estimated only very roughly. CoRe-PA is very useful when it is difficult or impossible to assign exact cost values to different types of coevolutionary events in advance. © 2010 Yeturu et al;licensee BioMed Central Ltd.

关键词： Costs

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News filtering and summarization on the Web

News filtering and summarization on the Web

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作者： Wu, Xindong Wu, Gong-Qing Xie, Fei Zhu, Zhu Hu, Xue-Gang Lu, Hao Li, Huiqian School of Computer Science and Information Engineering Hefei University of Technology China Zhejiang Taobao Network China Key Laboratory of Complex Systems and Intelligence Science Institute of Automation Chinese Academy of Sciences China Center for Social Computing and Parallel Systems Institute of Automation Chinese Academy of Sciences China

The news filtering and summarization (NFAS) system can automatically recognize Web news pages, retrieve each news page's title and news content, and extract key phrases. This extraction method substantially outper...

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Reports of the AAAI 2010 conference workshops

Reports of the AAAI 2010 conference workshops

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作者： Aha, David W. Boddy, Mark Bulitko, Vadim D'Avila Garcez, Artur S. Doshi, Prashant Edelkamp, Stefan Geib, Christopher Gmytrasiewicz, Piotr Goldman, Robert P. Halevy, Alon Hitzler, Pascal Isbell, Charles Josyula, Darsana Kaelbling, Leslie Pack Kersting, Kristian Kunda, Maithilee Lamb, Luis C. Marthi, Bhaskara McGreggor, Keith Mihalkova, Lilyana Nastase, Vivi Natarajan, Sriraam Provan, Gregory Raja, Anita Ram, Ashwin Riedl, Mark Russell, Stuart Sabharwal, Ashish Smaus, Jan-Georg Sukthankar, Gita Tuyls, Karl Van Der Meyden, Ron Adaptive Systems Section Naval Research Laboratory Washington DC United States Adventium Labs. Minneapolis MN United States Department of Computer Science University of Alberta Canada City University London United Kingdom University of Georgia United States University of Bremen Germany School of Informatics University of Edinburgh United Kingdom University of Illinois Chicago United States Smart Information Flow Technologies LLC Minneapolis MN United States Structured Data Group Google Research United States Department of Computer Science Wright State University Dayton OH United States School of Interactive Computing Georgia Institute of Technology Atlanta GA United States Department of Computer Science Bowie State University United States Department of Computer Science and Engineering Massachusetts Institute of Technology United States Statistical Relational Mining Group Fraunhofer IAIS Germany Department of Computer Science Federal University of Rio Grande Do sul Brazil Willow Garage Inc. CA United States Computer Science Department University of Maryland College Park United States Heidelberg Institute for Theoretical Studies Heidelberg Germany Department of Computer Science University of Wisconsin Madison United States University College Cork Ireland Cork Complex Systems Lab. Ireland Department of Software and Information Systems University of North Carolina Charlotte United States Department of Computer Science and Engineering University of California Berkeley United States Department of Computer Science Cornell University United States Institute for Computational Sustainability United States University of Freiburg Germany School of Electrical Engineering and Computer Science University of Central Florida United States Maastricht University Netherlands University of New South Wales NICTA Australia

The AAAI-10 workshop program was held on July 11-12, 2010, at the Westin Peachtree Plaza in Atlanta, Georgia. The workshop program included 13 workshops covering a wide range of topics in artificial intelligence. There were several presentations on particular formalisms for combining the levels of planning from the perspectives of classical planning, motion planning, POMDPs, search-based planning, and temporal logic-based constraints. Henry Lieberman from Massachusetts institute of Technology Media Laboratory presented work developing a platform for knowledge acquisition and usage from expert users, built upon experience with eliciting information from nonexperts in a collaborative manner. The objective of the AAAI Workshop on Goal-Directed Autonomy (GDA) was to encourage discussion and novel contributions on intelligent agents that can self-select their goals. Jeremy Baxter from QinetiQ focused on user interaction, while Nick Hawes described a goal-directed reasoning framework for controlling a mobile robot.

关键词： Motion planning

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Evolved cooperation and emergent communication structures in learning classifier based organic computing systems 09

Evolved cooperation and emergent communication structures in...

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11th Annual Genetic and Evolutionary Computation Conference, GECCO-2009

作者： Scheidler, Alexander Middendorf, Martin Parallel Computing and Complex Systems Group Faculty of Mathematics and Computer Science University of Leipzig Germany

ISBN: (纸本)9781605583259

In this paper we look at systems consisting of many autonomous components or agents which have only limited amount of resources (e.g. memory) but are able to communicate with each other. The aim of these systems is to solve classification problems (usually to classify binary strings). We incorporate a pittsburgh style learning classifier system into the agents and extend its possible actions by actions for passing the classification requests to other agents. We show that the system is able to overcome the limited resources of its parts by evolving cooperation between them. We take a deeper look at the structure of the generated rule sets and investigate the occurring communication patterns. © 2009 ACM.

关键词： Genetic algorithms

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Finding All sorting tandem duplication random loss operations

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20th Annual Symposium on Combinatorial Pattern Matching, CPM 2009

作者： Bernt, Matthias Chen, Ming-Chiang Merkle, Daniel Wang, Hung-Lung Chao, Kun-Mao Middendorf, Martin Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Germany Department of Computer Science and Information Engineering National Taiwan University Taiwan Department of Mathematics and Computer Science University of Southern Denmark Odense Denmark

ISBN: (纸本)3642024408

A tandem duplication random loss (TDRL) operation duplicates a contiguous segment of genes, followed by the loss of one copy of each of the duplicated genes. Although the importance of this operation is founded by several recent biological studies, it has been investigated only rarely from a theoretical point of view. Of particular interest are sorting TDRLs which are TDRLs that, when applied to a permutation representing a genome, reduce the distance towards another given permutation. The identification of sorting genome rearrangement operations in general is a key ingredient of many algorithms for reconstructing the evolutionary history of a set of species. In this paper we present methods to compute all sorting TDRLs for two given gene orders. In addition, a closed formula for the number of sorting TDRLs is derived and further properties of sorting TDRLs are investigated. It is also shown that the theoretical findings are useful for identifying unique sorting TDRL scenarios for mitochondrial gene orders. © 2009 Springer Berlin Heidelberg.

关键词： Genes

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On the Design of RNA Sequences for Realizing Extended Shapes

On the Design of RNA Sequences for Realizing Extended Shapes

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International Joint Conference on Bioinformatics, systems Biology and Intelligent computing, IJCBS

作者： Marc Hellmuth Daniel Merkle Martin Middendorf Interdisciplinary Centre of Bioinformatics Department of Computer Science University of Leipzig Leipzig Germany Department of Mathematics and Computer Science University of Southern Denmark Odense Denmark Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Leipzig Germany

It is known that for two given secondary structures (defined by position of base pairings) an RNA string can easily be found that can fold into both structures. But for more than two secondary structures this is not necessarily possible. Moreover, when four or more secondary structures are given the problem to determine the least number of positions, such that after the removal of all incident base pairs, a compatible RNA sequence can be found, is known to be NP-complete (\cite{real_shapes}). In this paper we introduce pseudo edges that are used to forbid that certain base pairs can bind and therefore can be used to define the properties of possible RNA secondary structures. We study the complexity of the problem to design an RNA sequence that can fold into different secondary structures each of them is described by a set of required and forbidden base pairs. We refine the NP-completeness results of \cite{real_shapes} and show an analoguous NP-completeness result for the realization problem concerning the removal of (pseudo) edges. We also present a polynomial time method for checking the realizability of extended shape graphs. Furthermore, we empirically analyze the influence of pseudo edges on the realizability for sets of random RNA sequences and for sets of aptamers.

关键词： RNA Shape Switches computer science Bioinformatics Sequences systems biology Intelligent systems Biology computing Concurrent computing

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SPP1148 booth: Hyperreconfigurable architectures

SPP1148 booth: Hyperreconfigurable architectures

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International Conference on Field Programmable Logic and Applications

作者： Sebastian Lange Martin Middendorf Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Germany

ISBN: (纸本)9781424419606

Dynamically reconfigurable hardware offers promising possibilities for flexible, computation intensive applications. With the technological advance of reconfigurable hardware came a rapid growth in the number of resources per chip requiring large amounts of data transfer per reconfiguration. Especially run-time reconfigurable applications, which make frequent use of reconfiguration, suffer from the growing overhead induced thereby. In this project, we investigate novel concepts for reconfigurable architectures that can dynamically reconfigure the actual reconfiguration potential to reduce the total amount of reconfiguration data that is necessary for a computation.

关键词： computer architecture Computational modeling Hardware Reconfigurable architectures Polynomials Control systems Conferences

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On the Reconfiguration Costs of Models for Partially Reconfigurable FPGAs

On the Reconfiguration Costs of Models for Partially Reconfi...

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Southern Conference on Programmable Logic

作者： Sebastian Lange Martin Middendorf Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Leipzig Germany

ISBN: (纸本)9781424419920

There exists several FPGA architectures that can be partially reconfigured at run-time. The advantage of partial run-time reconfiguration is that it allows to develop new algorithmic solutions for many applications. But a limiting factor for using frequent dynamic reconfiguration could be the reconfiguration overhead. In order to study the potential of frequent run-time reconfiguration it is interesting to investigate its costs and benefits from an abstract point of view and to develop new architectural concepts. In this paper, we provide a formal treatment of the reconfiguration costs and compare them for models of standard partially reconfigurable FPGAs and 2-level reconfigurable FPGAs.

关键词： Costs Field programmable gate arrays Switches Runtime computer architecture Reconfigurable architectures Reconfigurable logic parallel processing computer science Application software

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