[ { "key": "TM44Z5EW", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/TM44Z5EW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/TM44Z5EW", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Ferrer et al.", "parsedDate": "2006-01-01", "numChildren": 0 }, "data": { "key": "TM44Z5EW", "version": 1, "itemType": "journalArticle", "title": "Freezing of Binary Colloidal Systems for the Formation of Hierarchy Assemblies", "creators": [ { "creatorType": "author", "firstName": "Maria L.", "lastName": "Ferrer" }, { "creatorType": "author", "firstName": "Rocio", "lastName": "Esquembre" }, { "creatorType": "author", "firstName": "Ilida", "lastName": "Ortega" }, { "creatorType": "author", "firstName": "C. Reyes", "lastName": "Mateo" }, { "creatorType": "author", "firstName": "Francisco", "lastName": "del Monte" } ], "abstractNote": "Cryo-etch scanning electron microscopy (cryo-etch SEM) of aqueous gels composed of colloidal silica nanoparticles in the 1−40 nm range and liposomes of ∼200 nm gave unique morphologies. The aqueous gels are frozen at subcooled liquid nitrogen and fractured to obtain a fresh surface. High-vacuum sublimation of ice from the freshly exposed surface (etching) results in the formation of a hierarchy assembly, characterized by granular fences composed of colloidal silica and liposomes surrounded by empty areas in which amorphous ice originally resided. The biocompatible character of this ice segregation induced self-assembly (ISISA) process that allows for the preservation of the structural integrity of liposomes within the assembly is demonstrated by fluorescence anisotropy performed at the binary colloidal aqueous gels and differential scanning calorimetry and electron microscopy at the hierarchy assembly. The resulting assembly shows an interesting dual character, with one colloidal entity supporting the structure (e.g., silica) and the other providing functionality (e.g., liposomes).", "publicationTitle": "Chemistry of Materials", "publisher": "", "place": "", "date": "January 01, 2006", "volume": "18", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "554-559", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1021/cm052087z", "citationKey": "", "url": "http://dx.doi.org/10.1021/cm052087z", "accessDate": "2011-09-06T20:12:41Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ACS Publications", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "5MMCMFWM" ], "relations": {}, "dateAdded": "2011-09-06T20:50:48Z", "dateModified": "2011-09-06T20:50:48Z" } }, { "key": "P32UB9AQ", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/P32UB9AQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/P32UB9AQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Muuzuri and Vazquez-Otero", "parsedDate": "2008-07-14", "numChildren": 0 }, "data": { "key": "P32UB9AQ", "version": 1, "itemType": "conferencePaper", "title": "The CNN solution to the shortest-path-finder problem", "creators": [ { "creatorType": "author", "firstName": "A. P", "lastName": "Muuzuri" }, { "creatorType": "author", "firstName": "A.", "lastName": "Vazquez-Otero" } ], "abstractNote": "Algorithms to find the shortest path within the CNN context are a classical problem nowadays. An important attempt to solve this problem by parallel computing using the properties of autowaves was analyzed. Nevertheless, these solutions were unpractical as they required each cell of the system to remember when a wave went through it. In this text, anomalous properties of autowaves are used to solve the shortest-path-finder problem in a very robust, self-content way.", "proceedingsTitle": "11th International Workshop on Cellular Neural Networks and Their Applications, 2008. CNNA 2008", "conferenceName": "11th International Workshop on Cellular Neural Networks and Their Applications, 2008. CNNA 2008", "publisher": "IEEE", "place": "", "date": "14-16 July 2008", "eventPlace": "", "volume": "", "issue": "", "numberOfVolumes": "", "pages": "248-251", "series": "", "seriesNumber": "", "DOI": "10.1109/CNNA.2008.4588686", "ISBN": "978-1-4244-2089-6", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "IEEE Xplore", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Cellular neural networks", "type": 1 }, { "tag": "Chip scale packaging", "type": 1 }, { "tag": "Image processing", "type": 1 }, { "tag": "Mathematics", "type": 1 }, { "tag": "Orbital robotics", "type": 1 }, { "tag": "Parallel processing", "type": 1 }, { "tag": "Physics", "type": 1 }, { "tag": "Roads", "type": 1 }, { "tag": "Robustness", "type": 1 }, { "tag": "Very large scale integration", "type": 1 }, { "tag": "autowaves properties", "type": 1 }, { "tag": "cellular neural nets", "type": 1 }, { "tag": "cellular neural network", "type": 1 }, { "tag": "graph theory", "type": 1 }, { "tag": "mathematics computing", "type": 1 }, { "tag": "parallel computing", "type": 1 }, { "tag": "shortest-path-finder problem", "type": 1 } ], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "2UR9VFTU", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/2UR9VFTU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/2UR9VFTU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Adamatzky", "parsedDate": "2005", "numChildren": 0 }, "data": { "key": "2UR9VFTU", "version": 1, "itemType": "bookSection", "title": "Programming Reaction-Diffusion Processors", "creators": [ { "creatorType": "editor", "firstName": "Jean-Pierre", "lastName": "Banâtre" }, { "creatorType": "editor", "firstName": "Pascal", "lastName": "Fradet" }, { "creatorType": "editor", "firstName": "Jean-Louis", "lastName": "Giavitto" }, { "creatorType": "editor", "firstName": "Olivier", "lastName": "Michel" }, { "creatorType": "author", "firstName": "Andrew", "lastName": "Adamatzky" } ], "abstractNote": "", "bookTitle": "Unconventional Programming Paradigms", "series": "", "seriesNumber": "", "volume": "3566", "numberOfVolumes": "", "edition": "", "date": "2005", "publisher": "Springer Berlin Heidelberg", "place": "Berlin, Heidelberg", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "33-46", "ISBN": "978-3-540-27884-9", "DOI": "", "citationKey": "", "url": "http://www.springerlink.com.proxy1-bib.sdu.dk:2048/content/5kmmuayy2291nc0t/", "accessDate": "2011-09-06T20:20:44Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "J9UT5A28", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/J9UT5A28", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/J9UT5A28", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Adamatzky", "parsedDate": "2004-09", "numChildren": 0 }, "data": { "key": "J9UT5A28", "version": 1, "itemType": "journalArticle", "title": "Collision-based computing in Belousov-Zhabotinsky medium", "creators": [ { "creatorType": "author", "firstName": "Andrew", "lastName": "Adamatzky" } ], "abstractNote": "


A photosensitive sub-excitable Belousov-Zhabotinsky medium exhibits propagating wave fragments that preserve their shapes during substantial periods of time. In numerical studies we show that the medium is a computational universal architectureless system, if presence and absence of wave fragments are interpreted as truth values of Boolean variable. When two or more wave fragments collide they may annihilate, fuse, split or deviate from their original paths, thus values of the logical variables are changed and certain logical gates are realized in result of the collision. We demonstrate exact implementation of basic operations with signals and logical gates in Belousov-Zhabotinsky dynamic circuits. The findings provide a theoretical background for subsequent experimental implementation of collision-based, architectureless, dynamical computing devices in homogeneous active chemical media.

", "publicationTitle": "Chaos, Solitons & Fractals", "publisher": "", "place": "", "date": "September 2004", "volume": "21", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "1259-1264", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "16/j.chaos.2003.12.068", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S0960077903007215", "accessDate": "2011-09-06T19:41:49Z", "PMID": "", "PMCID": "", "ISSN": "0960-0779", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "0030", "rights": "", "extra": "", "tags": [], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "KJJ94T2B", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": 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"publicationTitle": "Naturwissenschaften", "publisher": "", "place": "", "date": "10/2002", "volume": "89", "issue": "10", "section": "", "partNumber": "", "partTitle": "", "pages": "474-478", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Naturwissenschaften", "DOI": "10.1007/s00114-002-0363-6", "citationKey": "", "url": "http://www.springerlink.com.proxy1-bib.sdu.dk:2048/content/47dh5t3kd48ycf95/", "accessDate": "2011-09-06T19:59:08Z", "PMID": "", "PMCID": "", "ISSN": "0028-1042", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "IFXV8HWW", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": 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Sciences", "publisher": "", "place": "", "date": "2001", "volume": "7", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "259-278", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.jstage.jst.go.jp/article/iis/7/2/7_259/_article/-char/en", "accessDate": "2011-09-06T20:29:32Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "J-Stage", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "4W5WJQEM", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/4W5WJQEM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/4W5WJQEM", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Kovalenko and Tikhonova", "parsedDate": "1992", "numChildren": 0 }, "data": { "key": "4W5WJQEM", "version": 1, "itemType": "journalArticle", "title": "Image processing using the Briggs-Raucher oscillating chemical reaction", "creators": [ { "creatorType": "author", "firstName": "A. S.", "lastName": "Kovalenko" }, { "creatorType": "author", "firstName": "L. P.", "lastName": "Tikhonova" } ], "abstractNote": "", "publicationTitle": "Reaction Kinetics & Catalysis Letters", "publisher": "", "place": "", "date": "7/1992", "volume": "48", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "99-103", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "React Kinet Catal Lett", "DOI": "10.1007/BF02070073", "citationKey": "", "url": "http://www.akademiai.com/content/r068jj8152116552/", "accessDate": "2011-09-06T19:44:26Z", "PMID": "", "PMCID": "", "ISSN": "0133-1736", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "0003", "rights": "", "extra": "", "tags": [], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "7M7RS3RE", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/7M7RS3RE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/7M7RS3RE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Scarle", "parsedDate": "2009-08", "numChildren": 0 }, "data": { "key": "7M7RS3RE", "version": 1, "itemType": "journalArticle", "title": "Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: Cardiac arrhythmias, re-entry and the Halting problem", "creators": [ { "creatorType": "author", "firstName": "Simon", "lastName": "Scarle" } ], "abstractNote": "


In the arsenal of tools that a computational modeller can bring to bare on the study of cardiac arrhythmias, the most widely used and arguably the most successful is that of an excitable medium, a special case of a reaction-diffusion model. These are used to simulate the internal chemical reactions of a cardiac cell and the diffusion of their membrane voltages. Via a number of different methodologies it has previously been shown that reaction-diffusion systems are at multiple levels Turing complete. That is, they are capable of computation in the same manner as a universal Turing machine. However, all such computational systems are subject to a limitation known as the Halting problem. By constructing a universal logic gate using a cardiac cell model, we highlight how the Halting problem therefore could limit what it is possible to predict about cardiac tissue, arrhythmias and re-entry.
All simulations for this work were carried out on the GPU of an XBox 360 development console, and we also highlight the great gains in computational power and efficiency produced by such general purpose processing on a GPU for cardiac simulations.

", "publicationTitle": "Computational Biology and Chemistry", "publisher": "", "place": "", "date": "August 2009", "volume": "33", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "253-260", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "16/j.compbiolchem.2009.05.001", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S1476927109000486", "accessDate": "2011-09-06T20:00:45Z", "PMID": "", "PMCID": "", "ISSN": "1476-9271", "archive": "", "archiveLocation": "", "shortTitle": "Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Cardiac arrhythmias", "type": 1 }, { "tag": "Excitable media", "type": 1 }, { "tag": "GPGPU", "type": 1 }, { "tag": "Halting problem", "type": 1 }, { "tag": "Heart", "type": 1 }, { "tag": "Re-entry", "type": 1 } ], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "2V4BBFC3", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/2V4BBFC3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/2V4BBFC3", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Motoike and Adamatzky", "parsedDate": "2005-04", "numChildren": 0 }, "data": { "key": "2V4BBFC3", "version": 1, "itemType": "journalArticle", "title": "Three-valued logic gates in reaction-diffusion excitable media", "creators": [ { "creatorType": "author", "firstName": "Ikuko N.", "lastName": "Motoike" }, { "creatorType": "author", "firstName": "Andrew", "lastName": "Adamatzky" } ], "abstractNote": "


It is well established now that excitable media are capable of implementing of a wide range of computational operations, from image processing to logical computation to navigation of robots. The findings published so far in the field of logical computation were concerned solely with realization of boolean logic. This imposed somewhat artificial limitations on a suitability of excitable media for logical reasoning and restricted a range of possible applications of these non-classical computational devices in the field of artificial intelligence. In the paper we go beyond binary logic and show how to implement three-valued logical operations in toy models of geometrically constrained excitable media. We realize several types of logical gates, including Lukasiewicz conjunction and disjunction, and Sobocinski conjunction in cellular automata and FitzHugh-Nagumo models of T-shaped excitable media.

", "publicationTitle": "Chaos, Solitons & Fractals", "publisher": "", "place": "", "date": "April 2005", "volume": "24", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "107-114", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "16/j.chaos.2004.07.021", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S0960077904004618", "accessDate": "2011-09-06T19:52:05Z", "PMID": "", "PMCID": "", "ISSN": "0960-0779", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "5KAZKZTR", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/5KAZKZTR", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/5KAZKZTR", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Adamatzky and De Lacy Costello", "parsedDate": "2002-10-14", "numChildren": 0 }, "data": { "key": "5KAZKZTR", "version": 1, "itemType": "journalArticle", "title": "Experimental logical gates in a reaction-diffusion medium: The XOR gate and beyond", "creators": [ { "creatorType": "author", "firstName": "Andrew", "lastName": "Adamatzky" }, { "creatorType": "author", "firstName": "Benjamin", "lastName": "De Lacy Costello" } ], "abstractNote": "We exploit the particulars of diffusive wave front interactions in certain types of two-reactant reaction-diffusion medium to construct a laboratory prototype of an XOR gate. In the design, the values of the logic variables are represented by the presence or absence of a precipitate, “wires” are constructed of a substrate loaded gel, and the computation is based on diffusive wave dynamics. We also discuss implementation of AND gate and study a three-valued composition, derived from the gate dynamic, and discuss possible logics that could be derived from this composition.", "publicationTitle": "Physical Review E", "publisher": "", "place": "", "date": "October 14, 2002", "volume": "66", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "046112", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Phys. Rev. E", "DOI": "10.1103/PhysRevE.66.046112", "citationKey": "", "url": "http://link.aps.org/doi/10.1103/PhysRevE.66.046112", "accessDate": "2011-09-06T19:41:13Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Experimental logical gates in a reaction-diffusion medium", "language": "", "libraryCatalog": "APS", "callNumber": "0034", "rights": "", "extra": "", "tags": [], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "HV6F3NZ4", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/HV6F3NZ4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/HV6F3NZ4", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Adamatzky et al.", "parsedDate": "2002-05-20", "numChildren": 0 }, "data": { "key": "HV6F3NZ4", "version": 1, "itemType": "journalArticle", "title": "Experimental reaction-diffusion pre-processor for shape recognition", "creators": [ { "creatorType": "author", "firstName": "Andrew", "lastName": "Adamatzky" }, { "creatorType": "author", "firstName": "Benjamin", "lastName": "de Lacy Costello" }, { "creatorType": "author", "firstName": "Norman M.", "lastName": "Ratcliffe" } ], "abstractNote": "


We have produced an experimental implementation of a massively-parallel reaction-diffusion processor which performs one of the most essential parts of shape recognition--construction of a skeleton. A skeleton is a unique, stable and invariant representation of a shape, therefore computation of the skeleton is an essential tool of computer vision. Skeleton computation is a typical [`]natural' spatial problem that can be solved with the use of biological, chemical or physical phenomena. One possible approach--a reaction-diffusion based computation--is explored in this Letter. A contour is represented by a concentration profile of one reagent, a planar substrate is mixed with another reagent. The reagent, representing the original contour diffuses to form a coloured phase in a reaction with the substrate-reagent. However, at sites where two diffusion wave fronts meet no coloured phase is formed and the substrate retains its uncoloured state. These loci of the computation space represent a skeleton of the given contour. In the Letter we only describe a laboratory prototype of a reaction-diffusion processor that computes a skeleton, no further tasks of image processing are undertaken, one could say we have designed an unconventional chemical pre-processor for shape recognition.

", "publicationTitle": "Physics Letters A", "publisher": "", "place": "", "date": "May 20, 2002", "volume": "297", "issue": "5-6", "section": "", "partNumber": "", "partTitle": "", "pages": "344-352", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "16/S0375-9601(02)00289-X", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S037596010200289X", "accessDate": "2011-09-06T19:57:35Z", "PMID": "", "PMCID": "", "ISSN": "0375-9601", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Chemical processor", "type": 1 }, { "tag": "Computing in reaction-diffusion medium", "type": 1 }, { "tag": "Physics-based computing", "type": 1 } ], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "KVVI8BB6", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/KVVI8BB6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/KVVI8BB6", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Agladze et al.", "parsedDate": "1997-08-01", "numChildren": 0 }, "data": { "key": "KVVI8BB6", "version": 1, "itemType": "journalArticle", "title": "Finding the optimal path with the aid of chemical wave", "creators": [ { "creatorType": "author", "firstName": "K.", "lastName": "Agladze" }, { "creatorType": "author", "firstName": "N.", "lastName": "Magome" }, { "creatorType": "author", "firstName": "R.", "lastName": "Aliev" }, { "creatorType": "author", "firstName": "T.", "lastName": "Yamaguchi" }, { "creatorType": "author", "firstName": "K.", "lastName": "Yoshikawa" } ], "abstractNote": "


It is shown that the optimal path in a two-dimensional vector field is deduced by the use of chemical wave in the Belousov-Zhabotinsky reaction (BZ reaction). We also reproduced our experimental result in a numerical simulation based on a two-variable reaction-diffusion equation. The present result provides a simple model for the future application of excitable media to parallel computing, i.e., an excitable medium serves as a self-organized parallel processor.

", "publicationTitle": "Physica D: Nonlinear Phenomena", "publisher": "", "place": "", "date": "August 1, 1997", "volume": "106", "issue": "3-4", "section": "", "partNumber": "", "partTitle": "", "pages": "247-254", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "16/S0167-2789(97)00049-3", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S0167278997000493", "accessDate": "2011-09-06T19:39:46Z", "PMID": "", "PMCID": "", "ISSN": "0167-2789", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "0052", "rights": "", "extra": "", "tags": [ { "tag": "BZ reaction", "type": 1 }, { "tag": "Chemical Computation", "type": 1 }, { "tag": "Excitable media", "type": 1 }, { "tag": "Optimal path", "type": 1 } ], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "I9C22HWJ", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/I9C22HWJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/I9C22HWJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Miyakawa et al.", "parsedDate": "1995", "numChildren": 0 }, "data": { "key": "I9C22HWJ", "version": 1, "itemType": "journalArticle", "title": "Light-Induced Spatio-Temporal Patterns in the Ferroin-Catalyzed Belousov-Zhabotinskii Reaction", "creators": [ { "creatorType": "author", "firstName": "Kenji", "lastName": "Miyakawa" }, { "creatorType": "author", "firstName": "Tatsuya", "lastName": "Noyori" }, { "creatorType": "author", "firstName": "Tadao", "lastName": "Okabe" }, { "creatorType": "author", "firstName": "Michiko", "lastName": "Mizoguchi" } ], "abstractNote": "Effects of illumination on the ferroin-catalyzed Belousov-Zhabotinskii reaction system were studied by using a visible light. The bulk chemical oscillation became slower in the illuminated area. Consequently, various chemical waves were initiated at the boundary between illuminated and non-illuminated areas. Such light-induced phenomena are similar to those observed in the tris(2,2'-bipyridine)ruthenium (II)-catalyzed system which is a typical light-sensitive photochemical one. Their behaviors strongly depended on the illumination time given on the basis of the period of oscillation in the non-illuminated area: in the case of illumination during one period, the change in contrast of the projected image occurred periodically. Under illumination during more than two periods, the contour of the projected image was formed at the boundary, and propagated to shrink towards the center of the projected image. ©1995 The Physical Society of Japan", "publicationTitle": "Journal of the Physical Society of Japan", "publisher": "", "place": "", "date": "1995", "volume": "64", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "3105-3111", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Phys. Soc. Jpn.", "DOI": "10.1143/JPSJ.64.3105", "citationKey": "", "url": "http://jpsj.ipap.jp/link?JPSJ/64/3105/", "accessDate": "2011-09-06T19:53:25Z", "PMID": "", "PMCID": "", "ISSN": "0031-9015", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Institute of Pure and Applied Physics", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "WKESDFGJ", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/WKESDFGJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/WKESDFGJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Petty", "numChildren": 0 }, "data": { "key": "WKESDFGJ", "version": 1, "itemType": "journalArticle", "title": "Spatiotemporal chemical dynamics in living cells: From information trafficking to cell physiology", "creators": [ { "creatorType": "author", "firstName": "Howard R.", "lastName": "Petty" } ], "abstractNote": "


Biological thought in the 20th century was dominated by the study of structures at increasingly minute levels. For biology to advance beyond structural reductionism and contribute its full measure to clinical care, living biological structures must be understood in the context of their collective chemical processes at the relevant chemical time-scales. Using high-speed fluorescence microscopy, we have studied intra- and inter-cellular signaling using shutter speeds (~100 ns) that remove the effects of wave motion and diffusion from optical images. By collecting a series of such images, stop-action movies of signal trafficking in living cells are created; these have revealed a new level of spatiotemporal chemical organization within cells. Numerous types of chemical waves have been found in living cells expressing a great variety of physical properties. In this article I will review some of these basic findings, discuss these events in the context of information trafficking, and illustrate the potential implications of this work in medicine.

", "publicationTitle": "Biosystems", "publisher": "", "place": "", "date": "February", "volume": "83", "issue": "2-3", "section": "", "partNumber": "", "partTitle": "", "pages": "217-224", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "16/j.biosystems.2005.05.018", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S0303264705001309", "accessDate": "2011-09-06T19:56:34Z", "PMID": "", "PMCID": "", "ISSN": "0303-2647", "archive": "", "archiveLocation": "", "shortTitle": "Spatiotemporal chemical dynamics in living cells", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Calcium", "type": 1 }, { "tag": "Cell signaling", "type": 1 }, { "tag": "Chemical waves", "type": 1 }, { "tag": "Metabolism", "type": 1 } ], "collections": [ "DS885D2G" ], "relations": {}, "dateAdded": "2011-09-06T20:49:58Z", "dateModified": "2011-09-06T20:49:58Z" } }, { "key": "4PKNF3TT", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/4PKNF3TT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/4PKNF3TT", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Miyakawa and Mizoguchi", "parsedDate": "1998", "numChildren": 0 }, "data": { "key": "4PKNF3TT", "version": 1, "itemType": "journalArticle", "title": "Responses of an immobilized-catalyst Belousov–Zabotinsky reaction system to electric fields", "creators": [ { "creatorType": "author", "firstName": "Kenji", "lastName": "Miyakawa" }, { "creatorType": "author", "firstName": "Michiko", "lastName": "Mizoguchi" } ], "abstractNote": "", "publicationTitle": "The Journal of Chemical Physics", "publisher": "", "place": "", "date": "1998", "volume": "109", "issue": "17", "section": "", "partNumber": "", "partTitle": "", "pages": "7462", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Chem. Phys.", "DOI": "10.1063/1.477368", "citationKey": "", "url": "http://link.aip.org/link/JCPSA6/v109/i17/p7462/s1&Agg=doi", "accessDate": "2011-09-06T20:06:40Z", "PMID": "", "PMCID": "", "ISSN": "00219606", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "8I5F873H" ], "relations": {}, "dateAdded": "2011-09-06T20:49:00Z", "dateModified": "2011-09-06T20:49:00Z" } }, { "key": "KNJXUX2B", "version": 1, "library": { "type": "group", "id": 47117, "name": "pattern formation reactions", "links": { "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/47117/items/KNJXUX2B", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/pattern_formation_reactions/items/KNJXUX2B", "type": "text/html" } }, "meta": { "createdByUser": { "id": 441677, "username": "mark-doerr", "name": "Mark Dörr", "links": { "alternate": { "href": "https://www.zotero.org/mark-doerr", "type": "text/html" } } }, "creatorSummary": "Miyazaki et al.", "parsedDate": "2004-04-01", "numChildren": 0 }, "data": { "key": "KNJXUX2B", "version": 1, "itemType": "journalArticle", "title": "Synchronized and intermittent oscillations observed in a sub Belousov-Zhabotinsky reactor under continuous mass flow from a main reactor", "creators": [ { "creatorType": "author", "firstName": "J.", "lastName": "Miyazaki" }, { "creatorType": "author", "firstName": "S.", "lastName": "Yoshioka" }, { "creatorType": "author", "firstName": "S.", "lastName": "Kinoshita" } ], "abstractNote": "


We have constructed a small ferroin-catalyzed Belousov-Zhabotinsky reactor connected with a main reactor through continuous mass flow. When each reactor is in an independent oscillating state, the activation energy of the oscillation frequency differs considerably from each other, which enables us to investigate the oscillating state of the former under precise control of the latter through coupling strength and frequency difference. With increasing flow rate, both synchronized and intermittent oscillations appear according to the sign of the frequency difference. A precursor exists near the synchronization, while the transition from resting to oscillating state takes place in a timely manner for the intermittent oscillation.

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It is shown that the optimal path in a two-dimensional vector field is deduced by the use of chemical wave in the Belousov-Zhabotinsky reaction (BZ reaction). We also reproduced our experimental result in a numerical simulation based on a two-variable reaction-diffusion equation. The present result provides a simple model for the future application of excitable media to parallel computing, i.e., an excitable medium serves as a self-organized parallel processor.

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