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Atom mapping with constraint programming

Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F Stadler, Christoph Flamm
2014 Algorithms for Molecular Biology  
Elementary chemical reactions feature a cyclic imaginary transition state (ITS) that imposes additional restrictions on the bijection between educt and product atoms that are not taken into account by  ...  Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products.  ...  Alexandre Varnek for providing the manually currated reaction data set from [34] in RDF format. Furthermore, we thank Heinz Ekker for comments and discussions on the initial project design.  ... 
doi:10.1186/s13015-014-0023-3 pmid:25484913 pmcid:PMC4256833 fatcat:dg3e5fa7iralffpk5bvkypw5cm

Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities

Konstantinos D. Vogiatzis, Mikhail V. Polynski, Justin K. Kirkland, Jacob Townsend, Ali Hashemi, Chong Liu, Evgeny A. Pidko
2018 Chemical Reviews  
This is followed by an overview of recent computational studies addressing the mechanistic complexity of catalytic processes by molecular catalysts based on 3d metals.  ...  The versatile reactivity and nontrivial electronic structure effects, common for systems based on 3d transition metals, introduce additional complexity that may represent a particular challenge to the  ...  Georgy Filonenko (TU Delft) for creating the table of contents image for this  ... 
doi:10.1021/acs.chemrev.8b00361 pmid:30376310 pmcid:PMC6396130 fatcat:qfvvgikmzvbktigbcsxzj5wixi

Software Replica of Minimal Living Processes

Hugues Bersini
2010 Origins of life and evolution of the biosphere  
information deemed not indispensable and have focused on the rule-based mechanisms making life possible, supposedly neutral with respect to their underlying material embodiment.  ...  Since John Von Neumann and Alan Turing pioneering works on self-replication and morphogenesis, proponents of artificial life have chosen to resolutely neglecting a lot of materialistic and quantitative  ...  Acknowledgments I thank Michel Morange for the invitation to participate to the 2008 meeting on life definition in Paris.  ... 
doi:10.1007/s11084-010-9190-5 pmid:20204519 fatcat:m46uvtkpnbh7bhjzmwctk4q43e

Polymer Synthesis: Theory and Practice

Matthias Rehahn Harald Cherdron
2020 Zenodo  
The origin of polymer science as a part of organic chemistry goes back to the end of the nineteenth century when chemists detected that the properties of many substances with colloidal properties are connected  ...  As a result of these and preferably of his own studies Hermann Staudinger (1881–1965) concluded in the early 1920s that substances like natural rubber, cellulose, and proteins but also many synthetic resins  ...  Ring-Opening Polymerization of Cyclic Ethers The ring-opening polymerization of cyclic ethers having 3-, 4-, and 5-membered rings (e.g., epoxides, oxetanes, THF) yields polymeric ethers.  ... 
doi:10.5281/zenodo.4022325 fatcat:6cen2wnwvffodm3w3eo3gongbi

Semantic networks

Fritz Lehmann
1992 Computers and Mathematics with Applications  
A semantic network is a graph of the structure of meaning.  ...  The conclusion argues for a synthesis of relational graph theory, graph-grmmnar theory and order theory based on semantic primitives and multiple intersecting inference hierarchies. • .. when controversies  ...  She created a thesaurus for organizing the concepts of a language into a hierarchy accessible to a computer, based on the classic Roger's Thesaurus which organizes concepts into a tree-structured taxonomy  ... 
doi:10.1016/0898-1221(92)90135-5 fatcat:4nli67lrsjdzdiu56i5ixwhm2a

CRISMA ICMS Architecture Document V2

Pascal Dihé
2014 Zenodo  
The main objective of this document is to provide an exhaustive specification of the architecture of the CRISMA Framework.  ...  This document is a deliverable of Sub-Project 3 (Integrated Crisis Modelling System) corresponding to WP32 (Crisis Modelling System Architecture), reporting on the results of the work performed in the  ...  to have/get common attributes and descriptions (like a location or the classification of a book in a library).  ... 
doi:10.5281/zenodo.1494827 fatcat:wvtc37n7frcwdcy6g2fcttg2b4

C2H [chapter]

2015 Encyclopedia of Astrobiology  
The cation C 3 H + is thought to play an important role in gas phase reactions in the ▶ interstellar medium that lead to the formation of small hydrocarbons.  ...  The neutral radical, C 3 H (▶ propynylidyne) can exist in both a linear (l-C 3 H) and a cyclic (c-C 3 H) form, and both these neutral species have been detected in interstellar molecular clouds.  ...  CO 2 þ 2H 2 O Respiration is an example of a biological combustion reaction.  ... 
doi:10.1007/978-3-662-44185-5_100142 fatcat:bkzmrhdghvhbdh7s3u4aem7aaa

Categorical Ontology of Complex Spacetime Structures: The Emergence of Life and Human Consciousness

I. C. Baianu, R. Brown, J. F. Glazebrook
2007 Axiomathes  
Primordial organism structures are predicted from the simplest metabolic-repair systems extended to self-replication through autocatalytic reactions.  ...  The emergence of consciousness and its existence seem dependent upon an extremely complex structural and functional unit with an asymmetric network topology and connectivitiesthe human brain-that developed  ...  An ontology based strictly on object classification may have little to offer from the point of view of its cognitive content.  ... 
doi:10.1007/s10516-007-9011-2 fatcat:m3kuram2fjcwze4mkmfxk2akwu

Themenheft zu Heft 5

(:Unkn) Unknown, Mediarep.Org, Jörg Schirra
2021 Image  
We also thank Sheelagh Carpendale, Pauline Jepp, Petra Neumann, and Martin Schwarz for fruitful discussions on the topic.  ...  Acknowledgements Ole Kniemeyer designed and implemented the programming language XL and the GroIMP software; without these tools and without his help this study would not have been possible.  ...  An RGG is a rewriting system operating on graphs instead of strings -here, a graph is a structure consisting of nodes and arcs (also called "edges") connecting some of these nodes, and it can have cyclic  ... 
doi:10.25969/mediarep/16743 fatcat:uh3wpotdmjgpjciazcj4cmbjie

The robot and the human. Where's their similarity limit?
Робот и Человек. Где находится предел их сходства?

Genrikh R. Ivanitskii
2018 Physics Uspekhi  
It is shown that the primary goal of robot±human collaboration is to ensure dynamic stability under varying environmental conditions.  ...  Compared with the robotic computer brain', its human counterpart has a multilevel hierarchical organization, with information processing occurring at all levels Ð from the quantum up to the social.  ...  Two publications by M I Rabinovich and co-workers,`N onlinear dynamics of the brain: emotions and cognition'' (2010) [14] and``Mathematics of consciousness'' (2017) [30] , gave me an additional impetus  ... 
doi:10.3367/ufne.2018.03.038302 fatcat:ffvdt33yabeefjwrrs5fjf4wl4

International editorial board

2005 Contact lens & anterior eye  
Abstract: The aim of this paper is to be determined the network capacity (number of necessary internal switching lines) based on detailed users' behaviour and demanded quality of service parameters in  ...  These parameters are requisite for maintenance demand level of network quality of service (QoS). Dependencies, based on the numericalanalytical results are shown graphically.  ...  In (Shu, 2000) , Augmented Transition Network based semantic data model is proposed. The ATN models the video based on scenes, shots and key frames using strings as a sequence of characters.  ... 
doi:10.1016/s1367-0484(05)00055-x fatcat:jcwauirmwvbipmmv625kxidgoe

Execution Models [chapter]

2006 Service-Oriented Computing  
the resulting graph is not cyclic.  ...  When new techniques improve the reaction times of organizations and people from weeks to seconds, they change the very structure of business.  ...  order. • The data in a value element must be an integer. • The data in an accuracy element must be an integer that is ≥ 0. • A scale must be one of the strings: Celsius, Fahrenheit, or Kelvin.  ... 
doi:10.1002/0470091509.ch10 fatcat:2jdemglma5gtre5xkxtzck45am

BME VIK Annual Research Report on Electrical Engineering and Computer Science 2016

Hassan Charaf, Gábor Harsányi, András Poppe, Sándor Imre, Bálint Kiss, Tamás Dabóczi, Gyula Katona, Lajos Nagy, Gábor Magyar, István Kiss
2017 Periodica Polytechnica Electrical Engineering and Computer Science  
These factors have positioned our Faculty as a significant source of knowledge transfer and a treasured partner in various cooperation activities.The current paper gives a brief account of the results  ...  We believe that this survey proves to be an informative summary about our scientific and technological contributions made in the year 2016.László Jakab (dean, BME VIK)János Levendovszky (vice-dean in charge  ...  Our prototype can easily scale beyond 100 Gbps on a single Intel blade even with complex OpenFlow pipelines [192] . We have also taken part in organizing several international conferences, e.g.  ... 
doi:10.3311/ppee.11067 fatcat:danqnppunnhq3mc2ns3qfhdwy4

The Evolution and Development of the Universe [article]

Clement Vidal, Charles Auffray, Alex H. Blin, Jean Chaline, Louis Crane, Thomas Durt, Borje Ekstig, Horace Fairlamb, Jan Greben, Rob Hengeveld, Francis Heylighen, Gerard Jagers op Akkerhuis, Giuseppe Longo (+9 others)
2010 arXiv   pre-print
This document is the Special Issue of the First International Conference on the Evolution and Development of the Universe (EDU 2008).  ...  , philosophy, physical constants, quantum darwinism, reduction, role of intelligent life, scale relativity, scientific evolution, self-organization, speciation, specification hierarchy, thermodynamics,  ...  EDU 2008 p129 The role of energy conservation and vacuum energy in the evolution of the universe 27 Thanks to Clément Vidal and John Smart for helpful comments on an earlier version of the paper. 8.  ... 
arXiv:0912.5508v2 fatcat:kaxv6ncc2vbebeyciwljjj2g6i

Stochastic Theory of Relativistic Particles Moving in a Quantum Field: I. Influence Functional and Langevin Equation [article]

Philip R. Johnson, B.L. Hu
2001 arXiv   pre-print
We treat a relativistically moving particle interacting with a quantum field from an open system viewpoint of quantum field theory by the method of influence functionals or closed-time-path coarse-grained  ...  This approach also discerns classical radiation reaction from quantum dissipation in the motion of a charged particle; only the latter is related to vacuum fluctuations in the quantum field by a fluctuation-dissipation  ...  In terms of Feynman diagrams, the graphs that are included in Γ 1 have only particle propagator (C39) lines.  ... 
arXiv:quant-ph/0012137v4 fatcat:d3qpzxt5ebcjzgll2okptwkrwm
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