A computational study of liposome logic: towards cellular computing from the bottom up View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-09

AUTHORS

James Smaldon, Francisco J. Romero-Campero, Francisco Fernández Trillo, Marian Gheorghe, Cameron Alexander, Natalio Krasnogor

ABSTRACT

In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This "liposome logic" approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in "top-down" synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of "bottom-up" liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie's stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up. More... »

PAGES

157-179

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s11693-010-9060-5

DOI

http://dx.doi.org/10.1007/s11693-010-9060-5

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1014398814

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/21886681


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0801", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Artificial Intelligence and Image Processing", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information and Computing Sciences", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of Nottingham", 
          "id": "https://www.grid.ac/institutes/grid.4563.4", 
          "name": [
            "School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, NG8 1BB, Nottingham, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Smaldon", 
        "givenName": "James", 
        "id": "sg:person.013261427665.08", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013261427665.08"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Nottingham", 
          "id": "https://www.grid.ac/institutes/grid.4563.4", 
          "name": [
            "School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, NG8 1BB, Nottingham, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Romero-Campero", 
        "givenName": "Francisco J.", 
        "id": "sg:person.01316772510.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316772510.33"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Nottingham", 
          "id": "https://www.grid.ac/institutes/grid.4563.4", 
          "name": [
            "School of Pharmacy, University of Nottingham, University Park, NG7 2RD, Nottingham, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Fern\u00e1ndez Trillo", 
        "givenName": "Francisco", 
        "id": "sg:person.01005731111.64", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01005731111.64"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Sheffield", 
          "id": "https://www.grid.ac/institutes/grid.11835.3e", 
          "name": [
            "Department of Computer Science, University of Sheffield, S1 4DP, Regent Court, 211 PortobelloSheffield, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gheorghe", 
        "givenName": "Marian", 
        "id": "sg:person.011355043215.85", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011355043215.85"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Nottingham", 
          "id": "https://www.grid.ac/institutes/grid.4563.4", 
          "name": [
            "School of Pharmacy, University of Nottingham, University Park, NG7 2RD, Nottingham, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Alexander", 
        "givenName": "Cameron", 
        "id": "sg:person.0655507567.45", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0655507567.45"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Nottingham", 
          "id": "https://www.grid.ac/institutes/grid.4563.4", 
          "name": [
            "School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, NG8 1BB, Nottingham, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Krasnogor", 
        "givenName": "Natalio", 
        "id": "sg:person.0620770042.97", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0620770042.97"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1038/msb4100202", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000486856"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/msb4100202", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000486856"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03461", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001000963", 
          "https://doi.org/10.1038/nature03461"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03461", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001000963", 
          "https://doi.org/10.1038/nature03461"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.1547", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001037177", 
          "https://doi.org/10.1038/nbt.1547"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.1547", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001037177", 
          "https://doi.org/10.1038/nbt.1547"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/b905791a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001537366"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/b905791a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001537366"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/anie.200801098", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004806487"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/anie.200603990", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009281500"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/chem.200802114", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009750125"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/adma.200700941", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010597342"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jconrel.2003.12.021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012769098"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-642-56196-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013689060", 
          "https://doi.org/10.1007/978-3-642-56196-2"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-642-56196-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013689060", 
          "https://doi.org/10.1007/978-3-642-56196-2"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bm801127d", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013902718"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/bm801127d", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013902718"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/b613201d", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014315243"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nchem.296", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014519255", 
          "https://doi.org/10.1038/nchem.296"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nchem.296", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014519255", 
          "https://doi.org/10.1038/nchem.296"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.physchem.58.032806.104637", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015207742"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35002125", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016534270", 
          "https://doi.org/10.1038/35002125"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35002125", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016534270", 
          "https://doi.org/10.1038/35002125"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35011540", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019498862", 
          "https://doi.org/10.1038/35011540"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/35011540", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019498862", 
          "https://doi.org/10.1038/35011540"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmat1333", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022128785", 
          "https://doi.org/10.1038/nmat1333"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmat1333", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022128785", 
          "https://doi.org/10.1038/nmat1333"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1145/1389095.1389134", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025403082"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04342", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025786828", 
          "https://doi.org/10.1038/nature04342"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04342", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025786828", 
          "https://doi.org/10.1038/nature04342"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04342", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025786828", 
          "https://doi.org/10.1038/nature04342"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/b406433j", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025933071"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00114-005-0056-z", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030060438", 
          "https://doi.org/10.1007/s00114-005-0056-z"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00114-005-0056-z", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030060438", 
          "https://doi.org/10.1007/s00114-005-0056-z"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt1356", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030162895", 
          "https://doi.org/10.1038/nbt1356"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/a908951i", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030187432"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1145/1506409.1506427", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030455500"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/msb4100073", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031450436"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/msb4100073", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031450436"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/b809333b", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031676350"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jconrel.2008.10.020", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031935682"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0307571101", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032119241"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt1006-1203", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033568084", 
          "https://doi.org/10.1038/nbt1006-1203"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt1006-1203", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033568084", 
          "https://doi.org/10.1038/nbt1006-1203"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0408236101", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036314159"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/b820313j", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036448513"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1039/b618473c", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036917824"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btl469", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038902414"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/3-540-46029-2_13", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045691071", 
          "https://doi.org/10.1007/3-540-46029-2_13"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bies.200900106", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046218994"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/bies.200900106", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046218994"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0006-3495(01)75737-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046593623"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1754-1611-2-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046794175", 
          "https://doi.org/10.1186/1754-1611-2-5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nnano.2007.188", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047332508", 
          "https://doi.org/10.1038/nnano.2007.188"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1754-1611-3-11", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049090779", 
          "https://doi.org/10.1186/1754-1611-3-11"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1145/1389095.1389153", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050464406"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/11880646_8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051539476", 
          "https://doi.org/10.1007/11880646_8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/11880646_8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051539476", 
          "https://doi.org/10.1007/11880646_8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1145/332833.332842", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052419132"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1098/rsif.2008.0205", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053580517"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ja056641h", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055840527"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ja056641h", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055840527"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ja8052688", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055859141"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ja8052688", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1055859141"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1063/1.474784", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1058058412"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1142/s0129054109006668", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062896959"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1209/0295-5075/30/4/001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1064230537"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.21236/ada457791", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1091559877"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2010-09", 
    "datePublishedReg": "2010-09-01", 
    "description": "In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This \"liposome logic\" approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in \"top-down\" synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of \"bottom-up\" liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie's stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1007/s11693-010-9060-5", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2771147", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2764185", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2771613", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2787490", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1038419", 
        "issn": [
          "1872-5325", 
          "1872-5333"
        ], 
        "name": "Systems and Synthetic Biology", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "3", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "4"
      }
    ], 
    "name": "A computational study of liposome logic: towards cellular computing from the bottom up", 
    "pagination": "157-179", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "44985cf573d44b6e521814de3fe2e16f75dfca2e5b22f5528154326c5157f9f4"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "21886681"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101300404"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s11693-010-9060-5"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1014398814"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s11693-010-9060-5", 
      "https://app.dimensions.ai/details/publication/pub.1014398814"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T10:35", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000349_0000000349/records_113667_00000000.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1007%2Fs11693-010-9060-5"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s11693-010-9060-5'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s11693-010-9060-5'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s11693-010-9060-5'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s11693-010-9060-5'


 

This table displays all metadata directly associated to this object as RDF triples.

279 TRIPLES      21 PREDICATES      78 URIs      21 LITERALS      9 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s11693-010-9060-5 schema:about anzsrc-for:08
2 anzsrc-for:0801
3 schema:author Ndf5e4e08d01546a6b64468d6b0c913c5
4 schema:citation sg:pub.10.1007/11880646_8
5 sg:pub.10.1007/3-540-46029-2_13
6 sg:pub.10.1007/978-3-642-56196-2
7 sg:pub.10.1007/s00114-005-0056-z
8 sg:pub.10.1038/35002125
9 sg:pub.10.1038/35011540
10 sg:pub.10.1038/nature03461
11 sg:pub.10.1038/nature04342
12 sg:pub.10.1038/nbt.1547
13 sg:pub.10.1038/nbt1006-1203
14 sg:pub.10.1038/nbt1356
15 sg:pub.10.1038/nchem.296
16 sg:pub.10.1038/nmat1333
17 sg:pub.10.1038/nnano.2007.188
18 sg:pub.10.1186/1754-1611-2-5
19 sg:pub.10.1186/1754-1611-3-11
20 https://doi.org/10.1002/adma.200700941
21 https://doi.org/10.1002/anie.200603990
22 https://doi.org/10.1002/anie.200801098
23 https://doi.org/10.1002/bies.200900106
24 https://doi.org/10.1002/chem.200802114
25 https://doi.org/10.1016/j.jconrel.2003.12.021
26 https://doi.org/10.1016/j.jconrel.2008.10.020
27 https://doi.org/10.1016/s0006-3495(01)75737-2
28 https://doi.org/10.1021/bm801127d
29 https://doi.org/10.1021/ja056641h
30 https://doi.org/10.1021/ja8052688
31 https://doi.org/10.1038/msb4100073
32 https://doi.org/10.1038/msb4100202
33 https://doi.org/10.1039/a908951i
34 https://doi.org/10.1039/b406433j
35 https://doi.org/10.1039/b613201d
36 https://doi.org/10.1039/b618473c
37 https://doi.org/10.1039/b809333b
38 https://doi.org/10.1039/b820313j
39 https://doi.org/10.1039/b905791a
40 https://doi.org/10.1063/1.474784
41 https://doi.org/10.1073/pnas.0307571101
42 https://doi.org/10.1073/pnas.0408236101
43 https://doi.org/10.1093/bioinformatics/btl469
44 https://doi.org/10.1098/rsif.2008.0205
45 https://doi.org/10.1142/s0129054109006668
46 https://doi.org/10.1145/1389095.1389134
47 https://doi.org/10.1145/1389095.1389153
48 https://doi.org/10.1145/1506409.1506427
49 https://doi.org/10.1145/332833.332842
50 https://doi.org/10.1146/annurev.physchem.58.032806.104637
51 https://doi.org/10.1209/0295-5075/30/4/001
52 https://doi.org/10.21236/ada457791
53 schema:datePublished 2010-09
54 schema:datePublishedReg 2010-09-01
55 schema:description In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This "liposome logic" approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in "top-down" synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of "bottom-up" liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie's stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up.
56 schema:genre research_article
57 schema:inLanguage en
58 schema:isAccessibleForFree true
59 schema:isPartOf N66a802db376644229f07a21c2e6a1aa4
60 N698ebca400744dffb58d2de2c609f6af
61 sg:journal.1038419
62 schema:name A computational study of liposome logic: towards cellular computing from the bottom up
63 schema:pagination 157-179
64 schema:productId N347caa425f9542e886f195462d89f07c
65 N48f896a152be4d82bba7effba2fea2de
66 Ncbbf5cc5def74dd3be668faeaadb38bb
67 Ne024a57db8e347edb20fa0d2046e8fbc
68 Ne76cc5bb82e343cb8d23ee439452a09d
69 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014398814
70 https://doi.org/10.1007/s11693-010-9060-5
71 schema:sdDatePublished 2019-04-11T10:35
72 schema:sdLicense https://scigraph.springernature.com/explorer/license/
73 schema:sdPublisher N0ad090f2187f4d6f89a149a00c70293c
74 schema:url http://link.springer.com/10.1007%2Fs11693-010-9060-5
75 sgo:license sg:explorer/license/
76 sgo:sdDataset articles
77 rdf:type schema:ScholarlyArticle
78 N0ad090f2187f4d6f89a149a00c70293c schema:name Springer Nature - SN SciGraph project
79 rdf:type schema:Organization
80 N0c962bba36164affba744c269aeb7931 rdf:first sg:person.01005731111.64
81 rdf:rest Nd462cbe12d4c4a788885deab067f1fe9
82 N347caa425f9542e886f195462d89f07c schema:name pubmed_id
83 schema:value 21886681
84 rdf:type schema:PropertyValue
85 N48f896a152be4d82bba7effba2fea2de schema:name doi
86 schema:value 10.1007/s11693-010-9060-5
87 rdf:type schema:PropertyValue
88 N66a802db376644229f07a21c2e6a1aa4 schema:volumeNumber 4
89 rdf:type schema:PublicationVolume
90 N698ebca400744dffb58d2de2c609f6af schema:issueNumber 3
91 rdf:type schema:PublicationIssue
92 N77d778429f95407394cdddcc8c58b6ec rdf:first sg:person.01316772510.33
93 rdf:rest N0c962bba36164affba744c269aeb7931
94 N7efa9797ff6148989c9807123cf3ca80 rdf:first sg:person.0655507567.45
95 rdf:rest Nc1c97898f3ff4f8a9d6cd1059fe6b1cc
96 Nc1c97898f3ff4f8a9d6cd1059fe6b1cc rdf:first sg:person.0620770042.97
97 rdf:rest rdf:nil
98 Ncbbf5cc5def74dd3be668faeaadb38bb schema:name readcube_id
99 schema:value 44985cf573d44b6e521814de3fe2e16f75dfca2e5b22f5528154326c5157f9f4
100 rdf:type schema:PropertyValue
101 Nd462cbe12d4c4a788885deab067f1fe9 rdf:first sg:person.011355043215.85
102 rdf:rest N7efa9797ff6148989c9807123cf3ca80
103 Ndf5e4e08d01546a6b64468d6b0c913c5 rdf:first sg:person.013261427665.08
104 rdf:rest N77d778429f95407394cdddcc8c58b6ec
105 Ne024a57db8e347edb20fa0d2046e8fbc schema:name nlm_unique_id
106 schema:value 101300404
107 rdf:type schema:PropertyValue
108 Ne76cc5bb82e343cb8d23ee439452a09d schema:name dimensions_id
109 schema:value pub.1014398814
110 rdf:type schema:PropertyValue
111 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
112 schema:name Information and Computing Sciences
113 rdf:type schema:DefinedTerm
114 anzsrc-for:0801 schema:inDefinedTermSet anzsrc-for:
115 schema:name Artificial Intelligence and Image Processing
116 rdf:type schema:DefinedTerm
117 sg:grant.2764185 http://pending.schema.org/fundedItem sg:pub.10.1007/s11693-010-9060-5
118 rdf:type schema:MonetaryGrant
119 sg:grant.2771147 http://pending.schema.org/fundedItem sg:pub.10.1007/s11693-010-9060-5
120 rdf:type schema:MonetaryGrant
121 sg:grant.2771613 http://pending.schema.org/fundedItem sg:pub.10.1007/s11693-010-9060-5
122 rdf:type schema:MonetaryGrant
123 sg:grant.2787490 http://pending.schema.org/fundedItem sg:pub.10.1007/s11693-010-9060-5
124 rdf:type schema:MonetaryGrant
125 sg:journal.1038419 schema:issn 1872-5325
126 1872-5333
127 schema:name Systems and Synthetic Biology
128 rdf:type schema:Periodical
129 sg:person.01005731111.64 schema:affiliation https://www.grid.ac/institutes/grid.4563.4
130 schema:familyName Fernández Trillo
131 schema:givenName Francisco
132 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01005731111.64
133 rdf:type schema:Person
134 sg:person.011355043215.85 schema:affiliation https://www.grid.ac/institutes/grid.11835.3e
135 schema:familyName Gheorghe
136 schema:givenName Marian
137 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011355043215.85
138 rdf:type schema:Person
139 sg:person.01316772510.33 schema:affiliation https://www.grid.ac/institutes/grid.4563.4
140 schema:familyName Romero-Campero
141 schema:givenName Francisco J.
142 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01316772510.33
143 rdf:type schema:Person
144 sg:person.013261427665.08 schema:affiliation https://www.grid.ac/institutes/grid.4563.4
145 schema:familyName Smaldon
146 schema:givenName James
147 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013261427665.08
148 rdf:type schema:Person
149 sg:person.0620770042.97 schema:affiliation https://www.grid.ac/institutes/grid.4563.4
150 schema:familyName Krasnogor
151 schema:givenName Natalio
152 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0620770042.97
153 rdf:type schema:Person
154 sg:person.0655507567.45 schema:affiliation https://www.grid.ac/institutes/grid.4563.4
155 schema:familyName Alexander
156 schema:givenName Cameron
157 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0655507567.45
158 rdf:type schema:Person
159 sg:pub.10.1007/11880646_8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051539476
160 https://doi.org/10.1007/11880646_8
161 rdf:type schema:CreativeWork
162 sg:pub.10.1007/3-540-46029-2_13 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045691071
163 https://doi.org/10.1007/3-540-46029-2_13
164 rdf:type schema:CreativeWork
165 sg:pub.10.1007/978-3-642-56196-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013689060
166 https://doi.org/10.1007/978-3-642-56196-2
167 rdf:type schema:CreativeWork
168 sg:pub.10.1007/s00114-005-0056-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1030060438
169 https://doi.org/10.1007/s00114-005-0056-z
170 rdf:type schema:CreativeWork
171 sg:pub.10.1038/35002125 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016534270
172 https://doi.org/10.1038/35002125
173 rdf:type schema:CreativeWork
174 sg:pub.10.1038/35011540 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019498862
175 https://doi.org/10.1038/35011540
176 rdf:type schema:CreativeWork
177 sg:pub.10.1038/nature03461 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001000963
178 https://doi.org/10.1038/nature03461
179 rdf:type schema:CreativeWork
180 sg:pub.10.1038/nature04342 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025786828
181 https://doi.org/10.1038/nature04342
182 rdf:type schema:CreativeWork
183 sg:pub.10.1038/nbt.1547 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001037177
184 https://doi.org/10.1038/nbt.1547
185 rdf:type schema:CreativeWork
186 sg:pub.10.1038/nbt1006-1203 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033568084
187 https://doi.org/10.1038/nbt1006-1203
188 rdf:type schema:CreativeWork
189 sg:pub.10.1038/nbt1356 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030162895
190 https://doi.org/10.1038/nbt1356
191 rdf:type schema:CreativeWork
192 sg:pub.10.1038/nchem.296 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014519255
193 https://doi.org/10.1038/nchem.296
194 rdf:type schema:CreativeWork
195 sg:pub.10.1038/nmat1333 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022128785
196 https://doi.org/10.1038/nmat1333
197 rdf:type schema:CreativeWork
198 sg:pub.10.1038/nnano.2007.188 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047332508
199 https://doi.org/10.1038/nnano.2007.188
200 rdf:type schema:CreativeWork
201 sg:pub.10.1186/1754-1611-2-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046794175
202 https://doi.org/10.1186/1754-1611-2-5
203 rdf:type schema:CreativeWork
204 sg:pub.10.1186/1754-1611-3-11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049090779
205 https://doi.org/10.1186/1754-1611-3-11
206 rdf:type schema:CreativeWork
207 https://doi.org/10.1002/adma.200700941 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010597342
208 rdf:type schema:CreativeWork
209 https://doi.org/10.1002/anie.200603990 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009281500
210 rdf:type schema:CreativeWork
211 https://doi.org/10.1002/anie.200801098 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004806487
212 rdf:type schema:CreativeWork
213 https://doi.org/10.1002/bies.200900106 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046218994
214 rdf:type schema:CreativeWork
215 https://doi.org/10.1002/chem.200802114 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009750125
216 rdf:type schema:CreativeWork
217 https://doi.org/10.1016/j.jconrel.2003.12.021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012769098
218 rdf:type schema:CreativeWork
219 https://doi.org/10.1016/j.jconrel.2008.10.020 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031935682
220 rdf:type schema:CreativeWork
221 https://doi.org/10.1016/s0006-3495(01)75737-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046593623
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1021/bm801127d schema:sameAs https://app.dimensions.ai/details/publication/pub.1013902718
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1021/ja056641h schema:sameAs https://app.dimensions.ai/details/publication/pub.1055840527
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1021/ja8052688 schema:sameAs https://app.dimensions.ai/details/publication/pub.1055859141
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1038/msb4100073 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031450436
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1038/msb4100202 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000486856
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1039/a908951i schema:sameAs https://app.dimensions.ai/details/publication/pub.1030187432
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1039/b406433j schema:sameAs https://app.dimensions.ai/details/publication/pub.1025933071
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1039/b613201d schema:sameAs https://app.dimensions.ai/details/publication/pub.1014315243
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1039/b618473c schema:sameAs https://app.dimensions.ai/details/publication/pub.1036917824
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1039/b809333b schema:sameAs https://app.dimensions.ai/details/publication/pub.1031676350
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1039/b820313j schema:sameAs https://app.dimensions.ai/details/publication/pub.1036448513
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1039/b905791a schema:sameAs https://app.dimensions.ai/details/publication/pub.1001537366
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1063/1.474784 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058058412
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1073/pnas.0307571101 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032119241
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1073/pnas.0408236101 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036314159
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1093/bioinformatics/btl469 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038902414
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1098/rsif.2008.0205 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053580517
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1142/s0129054109006668 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062896959
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1145/1389095.1389134 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025403082
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1145/1389095.1389153 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050464406
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1145/1506409.1506427 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030455500
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1145/332833.332842 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052419132
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1146/annurev.physchem.58.032806.104637 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015207742
268 rdf:type schema:CreativeWork
269 https://doi.org/10.1209/0295-5075/30/4/001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1064230537
270 rdf:type schema:CreativeWork
271 https://doi.org/10.21236/ada457791 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091559877
272 rdf:type schema:CreativeWork
273 https://www.grid.ac/institutes/grid.11835.3e schema:alternateName University of Sheffield
274 schema:name Department of Computer Science, University of Sheffield, S1 4DP, Regent Court, 211 PortobelloSheffield, UK
275 rdf:type schema:Organization
276 https://www.grid.ac/institutes/grid.4563.4 schema:alternateName University of Nottingham
277 schema:name School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, NG8 1BB, Nottingham, UK
278 School of Pharmacy, University of Nottingham, University Park, NG7 2RD, Nottingham, UK
279 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...